IB Chemistry on using ICT, 3D software with Jmol, Pymol, Rasmol and ACD for I...Lawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, ACD Lab and Rasmol. It discusses using these programs to measure properties like bond lengths, bond angles, hydrogen bonds and compare protein structures. Links are provided to download the software and view tutorials and examples of using the programs to analyze molecules from the Protein Data Bank and build organic structures. Limitations of computational modeling are also noted.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
1. The document discusses various molecular modeling software and databases that can be used to measure bond lengths, bond angles, bond strengths, and compare protein and DNA structures between different species.
2. It provides instructions on how to use modeling programs like Jmol, Pymol, Rasmol and ACD Labs to obtain 3D structures from the Protein Data Bank and measure various parameters.
3. The document suggests possible research questions focusing on how factors like element identity, bond type, substituents, and lone pair electrons affect bond angles and lengths based on data collected from both 3D modeling and databases.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
1. The document discusses measuring bond lengths, angles, and strengths using molecular modeling software like Jmol, PyMol, RasMol, and ACD Lab.
2. It also discusses using these software and databases like PDB, NCBI, UCSC and Ensembl to collect data on hydrogen bond distances between DNA/RNA base pairs across different species and cell types.
3. Limitations of molecular modeling are considered, like using multiple programs to validate results and checking against reliable databases like CRC and NIST. Accuracy of predicted structures from simulations alone is questioned.
IB Chemistry on ICT, 3D software, Jmol, Pymol, Rasmol and ACD for Internal As...Lawrence kok
The document discusses measuring properties of bonds such as length, angle, and strength using various 3D modeling software. It also covers using these programs to analyze protein and enzyme structures from the Protein Data Bank by inputting four-letter codes. Details are provided on tools for molecular modeling and 3D representation in Jmol, PyMol, RasMol, and ACD Labs. Spectroscopic and chemistry databases are listed for reference.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, Rasmol and ACD Lab. It discusses how to use these software to generate 3D structures from SMILES or PDB files, optimize structures, measure bond lengths, angles and distances. Possible research questions are outlined focusing on how factors like element identity, double bonds, substituents affect bond angles based on data collected from the software and databases. Limitations of using computational methods are also discussed.
IB Chemistry on using ICT, 3D software with Jmol, Pymol, Rasmol and ACD for I...Lawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, ACD Lab and Rasmol. It discusses using these programs to measure properties like bond lengths, bond angles, hydrogen bonds and compare protein structures. Links are provided to download the software and view tutorials and examples of using the programs to analyze molecules from the Protein Data Bank and build organic structures. Limitations of computational modeling are also noted.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
1. The document discusses various molecular modeling software and databases that can be used to measure bond lengths, bond angles, bond strengths, and compare protein and DNA structures between different species.
2. It provides instructions on how to use modeling programs like Jmol, Pymol, Rasmol and ACD Labs to obtain 3D structures from the Protein Data Bank and measure various parameters.
3. The document suggests possible research questions focusing on how factors like element identity, bond type, substituents, and lone pair electrons affect bond angles and lengths based on data collected from both 3D modeling and databases.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
1. The document discusses measuring bond lengths, angles, and strengths using molecular modeling software like Jmol, PyMol, RasMol, and ACD Lab.
2. It also discusses using these software and databases like PDB, NCBI, UCSC and Ensembl to collect data on hydrogen bond distances between DNA/RNA base pairs across different species and cell types.
3. Limitations of molecular modeling are considered, like using multiple programs to validate results and checking against reliable databases like CRC and NIST. Accuracy of predicted structures from simulations alone is questioned.
IB Chemistry on ICT, 3D software, Jmol, Pymol, Rasmol and ACD for Internal As...Lawrence kok
The document discusses measuring properties of bonds such as length, angle, and strength using various 3D modeling software. It also covers using these programs to analyze protein and enzyme structures from the Protein Data Bank by inputting four-letter codes. Details are provided on tools for molecular modeling and 3D representation in Jmol, PyMol, RasMol, and ACD Labs. Spectroscopic and chemistry databases are listed for reference.
IB Chemistry on ICT, 3D software, Jmol, Rasmol and Pymol for Internal AssessmentLawrence kok
The document provides a tutorial on using various 3D molecular modeling software like Jmol, Pymol, Rasmol and ACD Lab. It discusses how to use these software to generate 3D structures from SMILES or PDB files, optimize structures, measure bond lengths, angles and distances. Possible research questions are outlined focusing on how factors like element identity, double bonds, substituents affect bond angles based on data collected from the software and databases. Limitations of using computational methods are also discussed.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
The document discusses using 3D modeling software and databases to collect data on bond angles and lengths of alcohols and haloalkanes. Data was collected from Jmol, Pymol, Rasmol, ACD Lab and databases like CRC and RSC and averaged. Limitations of computational methods are that they assume non-interacting molecules in isolation. Data from multiple sources should be compared and experimental data is most reliable.
Patent Cheminformatics: Identification of key compounds in patentsSorel Muresan
Patents can contain valuable chemical and biological information not found in scientific journals. This document discusses extracting key compounds from patents, including identifying sources for full-text patents, extracting compounds from text, and predicting key compounds through methods like frequency of group analysis. Predicting key compounds is important as they are often the most biologically active and suitable for further development. The document provides examples of extracting known drug compounds like Bextra, Aciphex, and Aricept from early patents through these methods.
Getting the Big Picture by Joining up the SAR dotsSorel Muresan
Getting the Big Picture by Joining up the SAR dots
This document discusses challenges in integrating structure and bioactivity data at large scales due to the volume and complexity of unstructured data from various sources. It describes efforts to extract chemical entities from text using natural language processing and to standardize structures. The Chemistry Connect knowledge base aims to enable searching across internal and external datasets by developing a chemical dictionary and common representation of concepts.
Automated spelling correction to improve recall rates of name-to-structure to...Sorel Muresan
This document discusses using automated spelling correction to improve the recall rates of name-to-structure tools for chemical text mining. It notes that the biggest cause of missing compounds when extracting chemical entities is the presence of typographical errors. The document introduces CaffeineFix, a chemical nomenclature aware automatic spell checker, that can significantly improve recall rates as a pre-processing step by correcting OCR and other errors in compound names found in patents and other texts.
Deep Purple: Discolouration in CBD productsMarkus Roggen
Presentation at ACS Spring 2022 conference.
Recently, there has been a flood of cannabidiol (CBD)-containing products, with divers marketing claims for a plethora of use cases. With this new market segment, regulatory oversight is still developing, and label claims of CBD concentration is often verifiable. CBD is unstable in solution and some CBD products are anecdotally reported to turn purple on storage; however, the decomposition products of CBD are mostly unknown.
Delic Lab embarked on a long and painstaking hunt for those decomposition products, established their identity through complementary chemical methods and established reaction pathways between them.
We will present our findings about common CBD oxidation products, who those are highly photochemically unstable and decomposes rapidly. Decomposition leads to a multitude of new cannabinoid derivatives.
Automated Extraction of Reactions from the Patent Literaturedan2097
We have created a pipeline of recently enhanced open source components for extracting chemical reactions from full text chemical literature. OSCAR4 is used to recognise chemical entities and resolve to structures where appropriate. OPSIN is used to resolve systematic chemical names to structures. Chemical Tagger performs part of speech tagging allowing the interpretation of phrases in chemical syntheses. The final output is a semantic representation (chemical components and their roles, reaction conditions, actions including workup, yield and properties of the product). We then attempt to map all atoms in the product(s) to reactants. If successful we also attempt to calculate the stoichiometry of the reaction. The system has been deployed on over 56,000 USPTO patents published since 2008. The level of recall is useful and most extracted reactions make chemical sense. The pipeline is generally applicable to reactions in chemical literature including journals and theses.
IB Chemistry on Mass Spectrometry, Index Hydrogen Deficiency and IsotopesLawrence kok
The document discusses index hydrogen deficiency (IHD), which is a measure of unsaturation in molecules. IHD is calculated based on the number of hydrogen atoms fewer than would be present in a saturated molecule with the same number of carbon atoms. The document provides examples of calculating IHD for various molecules containing double bonds, rings, and heteroatoms like nitrogen. It also describes how mass spectrometry can be used to determine IHD and identify molecular structures based on their fragmentation patterns.
IB Chemistry on Mass Spectrometry, Index Hydrogen Deficiency and IsotopesLawrence kok
This document provides a tutorial on mass spectrometry, isotopes identification, and index hydrogen deficiency (IHD). It defines IHD as the degree of unsaturation in a molecule, and explains how to calculate IHD based on the number of double bonds, rings, or other functional groups present. It also discusses how the presence of isotopes affects relative atomic mass calculations. Mass spectrometry techniques are described for identifying isotopes and abundances, calculating relative atomic masses, determining molecular structure, and distinguishing between structural isomers.
IB Chemistry on Stereoisomers, E/Z, Cis Trans, Geometric, Optical and Polarim...Lawrence kok
There are two types of isomerism: structural isomerism and stereoisomerism. Structural isomers have the same molecular formula but different structural formulas or arrangements of atoms. Stereoisomers have the same molecular formula and structural formula but different spatial arrangements of atoms. Examples of stereoiosmers include geometric isomers, which require a double bond or ring structure to prevent bond rotation, and optical isomers. The E/Z or Cahn-Ingold-Prelog system is used to name geometric isomers based on atomic mass priorities of substituents.
IB Chemistry on Stereoisomers, E/Z, Cis Trans, Geometric, Optical Isomer and ...Lawrence kok
- Stereoisomers are molecules with the same molecular formula but different arrangements of atoms in space. There are two main types of isomerism: positional isomers and stereoisomers.
- Stereoisomers include geometric isomers and optical isomers. Geometric isomers have the same connectivity but different spatial arrangements, and require a double bond or ring structure. Cis isomers have substituents on the same side, trans on opposite sides.
- The E/Z system names geometric isomers based on atomic number priorities using Cahn-Ingold-Prelog rules, with "Z" denoting same-side priority and "E" opposite sides.
IB Chemistry Nucleophilic Substitution, SN1, SN2 and protic solventLawrence kok
This document describes organic functional groups including alkanes, alkenes, alcohols, esters, and their characteristic properties and reactions. Alkanes are saturated hydrocarbons with single carbon-carbon bonds and have low reactivity. Alkenes are unsaturated hydrocarbons with carbon-carbon double bonds and undergo addition reactions more readily than alkanes. Alcohols contain an -OH group and can be oxidized to aldehydes, ketones, or carboxylic acids. Esters are formed from the condensation reaction between carboxylic acids and alcohols, producing water.
IB Chemistry on Electrophilic Addition and Synthetic routesLawrence kok
1) Halogenoalkanes undergo nucleophilic substitution reactions where the halogen is replaced. Alkenes undergo electrophilic addition reactions where atoms or groups are added across the carbon-carbon double bond.
2) Electrophiles are electron deficient species that accept electron pairs from nucleophiles. Common electrophiles include halogen atoms, protons, and carbocations.
3) The reactivity of alkenes is due to the weak pi bond and presence of electron-rich pi electrons on the carbon atoms of the double bond, which attract electrophiles for addition reactions.
IB Chemistry on Electrophilic Addition and Synthetic routesLawrence kok
The document provides a tutorial on electrophilic addition and synthetic routes. It discusses electrophiles, nucleophiles, and various organic reactions including addition, substitution, and free radical reactions. It specifically examines electrophilic addition reactions of alkenes and the reactivity of symmetrical versus asymmetrical alkenes in these reactions.
IB Chemistry on Organic nomenclature and functional groups.Lawrence kok
The document discusses organic functional groups and their naming conventions. It provides the suffixes used to name different classes of organic compounds based on their functional groups, including -ane for alkanes, -ene for alkenes, -yne for alkynes, -ol for alcohols, and -one for ketones. It also gives examples of compound names and formulas for different functional groups like ethane for alkanes and ethene for alkenes.
IB Chemistry on Homologous series, Functional gp and nomenclatureLawrence kok
This document provides a tutorial on organic chemistry nomenclature, functional groups, and homologous series. It includes:
- Definitions of homologous series for alkanes as compounds that differ by CH2 groups, have the same functional group and similar properties, and names ending in -ane.
- Examples of common alkanes from methane to nonane with their IUPAC names, structural formulas, and molecular formulas.
- Information on other functional groups like alkenes and their homologous series with examples.
IB Chemistry on Homologous series and functional groups of organic moleculesLawrence kok
- The document provides a tutorial on homologous series and functional groups in organic chemistry.
- Homologous series are classes of compounds that differ by a -CH2- group and have similar chemical properties. Alkanes and alkenes are examples of homologous series.
- Alkanes have the general formula CnH2n+2 and end in -ane. Alkenes have the general formula CnH2n and end in -ene.
- Tables are provided that list common homologous series with their functional groups, suffixes, examples, and molecular formulas.
IB Chemistry on ICT, 3D software, Jmol, Pymol and Rasmol for Internal AssessmentLawrence kok
The document discusses using 3D modeling software and databases to collect data on bond angles and lengths of alcohols and haloalkanes. Data was collected from Jmol, Pymol, Rasmol, ACD Lab and databases like CRC and RSC and averaged. Limitations of computational methods are that they assume non-interacting molecules in isolation. Data from multiple sources should be compared and experimental data is most reliable.
Patent Cheminformatics: Identification of key compounds in patentsSorel Muresan
Patents can contain valuable chemical and biological information not found in scientific journals. This document discusses extracting key compounds from patents, including identifying sources for full-text patents, extracting compounds from text, and predicting key compounds through methods like frequency of group analysis. Predicting key compounds is important as they are often the most biologically active and suitable for further development. The document provides examples of extracting known drug compounds like Bextra, Aciphex, and Aricept from early patents through these methods.
Getting the Big Picture by Joining up the SAR dotsSorel Muresan
Getting the Big Picture by Joining up the SAR dots
This document discusses challenges in integrating structure and bioactivity data at large scales due to the volume and complexity of unstructured data from various sources. It describes efforts to extract chemical entities from text using natural language processing and to standardize structures. The Chemistry Connect knowledge base aims to enable searching across internal and external datasets by developing a chemical dictionary and common representation of concepts.
Automated spelling correction to improve recall rates of name-to-structure to...Sorel Muresan
This document discusses using automated spelling correction to improve the recall rates of name-to-structure tools for chemical text mining. It notes that the biggest cause of missing compounds when extracting chemical entities is the presence of typographical errors. The document introduces CaffeineFix, a chemical nomenclature aware automatic spell checker, that can significantly improve recall rates as a pre-processing step by correcting OCR and other errors in compound names found in patents and other texts.
Deep Purple: Discolouration in CBD productsMarkus Roggen
Presentation at ACS Spring 2022 conference.
Recently, there has been a flood of cannabidiol (CBD)-containing products, with divers marketing claims for a plethora of use cases. With this new market segment, regulatory oversight is still developing, and label claims of CBD concentration is often verifiable. CBD is unstable in solution and some CBD products are anecdotally reported to turn purple on storage; however, the decomposition products of CBD are mostly unknown.
Delic Lab embarked on a long and painstaking hunt for those decomposition products, established their identity through complementary chemical methods and established reaction pathways between them.
We will present our findings about common CBD oxidation products, who those are highly photochemically unstable and decomposes rapidly. Decomposition leads to a multitude of new cannabinoid derivatives.
Automated Extraction of Reactions from the Patent Literaturedan2097
We have created a pipeline of recently enhanced open source components for extracting chemical reactions from full text chemical literature. OSCAR4 is used to recognise chemical entities and resolve to structures where appropriate. OPSIN is used to resolve systematic chemical names to structures. Chemical Tagger performs part of speech tagging allowing the interpretation of phrases in chemical syntheses. The final output is a semantic representation (chemical components and their roles, reaction conditions, actions including workup, yield and properties of the product). We then attempt to map all atoms in the product(s) to reactants. If successful we also attempt to calculate the stoichiometry of the reaction. The system has been deployed on over 56,000 USPTO patents published since 2008. The level of recall is useful and most extracted reactions make chemical sense. The pipeline is generally applicable to reactions in chemical literature including journals and theses.
IB Chemistry on Mass Spectrometry, Index Hydrogen Deficiency and IsotopesLawrence kok
The document discusses index hydrogen deficiency (IHD), which is a measure of unsaturation in molecules. IHD is calculated based on the number of hydrogen atoms fewer than would be present in a saturated molecule with the same number of carbon atoms. The document provides examples of calculating IHD for various molecules containing double bonds, rings, and heteroatoms like nitrogen. It also describes how mass spectrometry can be used to determine IHD and identify molecular structures based on their fragmentation patterns.
IB Chemistry on Mass Spectrometry, Index Hydrogen Deficiency and IsotopesLawrence kok
This document provides a tutorial on mass spectrometry, isotopes identification, and index hydrogen deficiency (IHD). It defines IHD as the degree of unsaturation in a molecule, and explains how to calculate IHD based on the number of double bonds, rings, or other functional groups present. It also discusses how the presence of isotopes affects relative atomic mass calculations. Mass spectrometry techniques are described for identifying isotopes and abundances, calculating relative atomic masses, determining molecular structure, and distinguishing between structural isomers.
IB Chemistry on Stereoisomers, E/Z, Cis Trans, Geometric, Optical and Polarim...Lawrence kok
There are two types of isomerism: structural isomerism and stereoisomerism. Structural isomers have the same molecular formula but different structural formulas or arrangements of atoms. Stereoisomers have the same molecular formula and structural formula but different spatial arrangements of atoms. Examples of stereoiosmers include geometric isomers, which require a double bond or ring structure to prevent bond rotation, and optical isomers. The E/Z or Cahn-Ingold-Prelog system is used to name geometric isomers based on atomic mass priorities of substituents.
IB Chemistry on Stereoisomers, E/Z, Cis Trans, Geometric, Optical Isomer and ...Lawrence kok
- Stereoisomers are molecules with the same molecular formula but different arrangements of atoms in space. There are two main types of isomerism: positional isomers and stereoisomers.
- Stereoisomers include geometric isomers and optical isomers. Geometric isomers have the same connectivity but different spatial arrangements, and require a double bond or ring structure. Cis isomers have substituents on the same side, trans on opposite sides.
- The E/Z system names geometric isomers based on atomic number priorities using Cahn-Ingold-Prelog rules, with "Z" denoting same-side priority and "E" opposite sides.
IB Chemistry Nucleophilic Substitution, SN1, SN2 and protic solventLawrence kok
This document describes organic functional groups including alkanes, alkenes, alcohols, esters, and their characteristic properties and reactions. Alkanes are saturated hydrocarbons with single carbon-carbon bonds and have low reactivity. Alkenes are unsaturated hydrocarbons with carbon-carbon double bonds and undergo addition reactions more readily than alkanes. Alcohols contain an -OH group and can be oxidized to aldehydes, ketones, or carboxylic acids. Esters are formed from the condensation reaction between carboxylic acids and alcohols, producing water.
IB Chemistry on Electrophilic Addition and Synthetic routesLawrence kok
1) Halogenoalkanes undergo nucleophilic substitution reactions where the halogen is replaced. Alkenes undergo electrophilic addition reactions where atoms or groups are added across the carbon-carbon double bond.
2) Electrophiles are electron deficient species that accept electron pairs from nucleophiles. Common electrophiles include halogen atoms, protons, and carbocations.
3) The reactivity of alkenes is due to the weak pi bond and presence of electron-rich pi electrons on the carbon atoms of the double bond, which attract electrophiles for addition reactions.
IB Chemistry on Electrophilic Addition and Synthetic routesLawrence kok
The document provides a tutorial on electrophilic addition and synthetic routes. It discusses electrophiles, nucleophiles, and various organic reactions including addition, substitution, and free radical reactions. It specifically examines electrophilic addition reactions of alkenes and the reactivity of symmetrical versus asymmetrical alkenes in these reactions.
IB Chemistry on Organic nomenclature and functional groups.Lawrence kok
The document discusses organic functional groups and their naming conventions. It provides the suffixes used to name different classes of organic compounds based on their functional groups, including -ane for alkanes, -ene for alkenes, -yne for alkynes, -ol for alcohols, and -one for ketones. It also gives examples of compound names and formulas for different functional groups like ethane for alkanes and ethene for alkenes.
IB Chemistry on Homologous series, Functional gp and nomenclatureLawrence kok
This document provides a tutorial on organic chemistry nomenclature, functional groups, and homologous series. It includes:
- Definitions of homologous series for alkanes as compounds that differ by CH2 groups, have the same functional group and similar properties, and names ending in -ane.
- Examples of common alkanes from methane to nonane with their IUPAC names, structural formulas, and molecular formulas.
- Information on other functional groups like alkenes and their homologous series with examples.
IB Chemistry on Homologous series and functional groups of organic moleculesLawrence kok
- The document provides a tutorial on homologous series and functional groups in organic chemistry.
- Homologous series are classes of compounds that differ by a -CH2- group and have similar chemical properties. Alkanes and alkenes are examples of homologous series.
- Alkanes have the general formula CnH2n+2 and end in -ane. Alkenes have the general formula CnH2n and end in -ene.
- Tables are provided that list common homologous series with their functional groups, suffixes, examples, and molecular formulas.
IB Chemistry on Homologous series and functional groups of organic moleculesLawrence kok
The document discusses organic functional groups and their IUPAC nomenclature rules. It defines classes of organic compounds such as alkanes, alkenes, alkynes, alcohols, ethers, ketones, aldehydes, carboxylic acids, esters, amides, amines, nitriles and haloalkanes based on their functional groups. It provides examples and molecular formulas for different functional groups and discusses IUPAC nomenclature rules for systematically naming organic compounds including identifying the parent chain, functional group, substituents and their positions.
IB Chemistry on Nucleophilic Substitution, SN1, SN2 and protic solventLawrence kok
This document provides a tutorial on organic chemistry reactions, specifically nucleophilic substitution reactions (SN1 and SN2) and the reactivity of functional groups. It discusses the properties and reactions of alkanes, alkenes, alcohols, aldehydes, ketones, carboxylic acids, and esters. Key reactions covered include combustion, halogenation, oxidation, esterification, and polymerization. Reaction mechanisms and conditions are explained for common transformations of functional groups like alcohol oxidation and ester synthesis.
IB Chemistry on Structural Isomers and Benzene StructureLawrence kok
The document discusses organic functional groups and their naming conventions. It provides examples of common organic compound classes including alkanes, alkenes, alkynes, alcohols, ethers, ketones, aldehydes, carboxylic acids, esters, amides, amines, nitriles, and halogenoalkanes. It also discusses IUPAC nomenclature rules for systematically naming organic molecules based on functional groups, carbon chain length and position of substituents. Additionally, it briefly touches on isomerism, which refers to compounds with the same molecular formula but different structural or spatial arrangements of atoms.
IB Chemistry on Free radical substitution, Addition and Nucleophilic substitu...Lawrence kok
This document describes various classes of organic compounds including alkanes, alkenes, alcohols, esters, and their properties. Alkanes are saturated hydrocarbons with the general formula CnH2n+2. Alkenes are unsaturated hydrocarbons containing carbon-carbon double bonds with the general formula CnH2n. Alcohols contain an -OH functional group and have the general formula CnH2n+1OH. Esters are formed from the condensation reaction between carboxylic acids and alcohols, producing water as a byproduct. Common chemical reactions for each class are also outlined such as combustion, addition, oxidation, and esterification
Basic Experiment of bioinformatics laboratory.
-Searching basics, AND, OR, NOT, “keywords together”, *
-Searching PMC and PubMed Using Authors name, fields, limits
-Retrieving protein sequences using UniProt and creating multi-fasta files
-Retrieving relevant DNA sequences using nucleotide and creating multi fasta-file. (search by ldh1 NOT hypothetical)
-Performing DNA and protein BLAST and analyzing result
-Pairwise alignment (global, end gap free), calculate identities, dotplot using BioEdit
-Nucleotide composition, complement, reverse complement, DNA to RNA, translate, restriction map, six frame translation using BioEdit
-Multiple sequence analysis using BioEdit
-Tree Generation with MEGA
-Working with single protein sequence: Analyzing protein composition (pepdigest, pepstats), Protein secondary structure by mEmboss: (garnier for protein secondary structure), helixturnhelix for motifs, pepcoil for coiled coil regions
-RNA structure prediction using RNAstructure
This document discusses different levels of protein structure from primary to quaternary structure. It explains that primary structure refers to the amino acid sequence of a protein. Secondary structure describes local folding patterns like alpha helices and beta sheets. Tertiary structure is the overall 3D shape of a single protein chain that results from folding. Quaternary structure involves the shape and interactions of multiple protein subunits. The document provides examples and diagrams to illustrate each level of structure and how they relate to determining a protein's function.
This document discusses various topics relating to protein structure and bioinformatics. It begins with an overview of protein structure and why understanding protein structure is important. It then discusses the different levels of protein structure from primary to quaternary structure. Methods for determining protein structure like X-ray crystallography and NMR are mentioned. Databases for storing protein structures like the Protein Data Bank are also summarized. The document touches on topics like protein folding, domains, membrane protein topology, and secondary structure prediction methods.
EUGM15 - George Papadatos, Mark Davies, Nathan Dedman (EMBL-EBI): SureChEMBL:...ChemAxon
SureChEMBL is a new resource provided by the European Bioinformatics Institute (EMBL-EBI) that annotates, extracts and indexes chemistry from full text patent documents by means of continuous, automated text and image mining. SureChEMBL is perhaps the only open, freely available, live patent chemistry resource available, in a field that has been traditionally commercial.
Since its launch last September, the SureChEMBL interface provides sophisticated keyword and chemistry-based querying and exporting functionality against a corpus of more than 16 million compounds extracted from 13 million patent documents. Both the interface and the underlying data pipeline leverage extensively ChemAxon technologies for name to structure conversion, as well as compound standardisation, registration and searching.
In addition to providing an overview of the system, recent developments and improvements will be described. These include the introduction of various data interexchange and exporting options, such as flat files and a data feed client. Furthermore, our future plans for the SureChEMBL system will be outlined. To date, such plans include complementing the chemical annotations with biological ones, covering genes, proteins, diseases and indications. Furthermore, we are planning to further enrich the chemical annotations with a relevance score, indicating their importance in the patent document.
Biological literature mining - from information retrieval to biological disco...Lars Juhl Jensen
14th International Conference on Intelligent Systems for Molecular Biology, Tutorial, Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006
This is the webinar presented on the 14th April as part of the Ensembl Online Webinar series. You can view the recorded webinar on the Ensembl Helpdesk youtube channel https://www.youtube.com/watch?v=blbhuqiiDoA
This document contains an agenda for bioinformatics lessons covering various topics like biological databases, sequence similarity, sequence alignments, database searching, phylogenetics, protein structure, gene prediction, and bioinformatics applications in drug discovery. It also discusses ongoing bioinformatics research projects and ambitions to publish peer-reviewed work. Finally, it provides background on protein structure, levels of protein structure from primary to tertiary, and experimental methods like X-ray crystallography used to determine protein structures.
Cox2007-Protein_fabrication_automationJ. Colin Cox
Protein fabrication automation (PFA) is a process that facilitates the rapid de novo construction of any desired open reading frame (ORF) from synthetic oligonucleotides with low effort, high speed, and little human interaction. PFA integrates software for sequence design and data management, a liquid-handling robot, a robust inside-out nucleation (ION) PCR scheme for gene assembly from oligonucleotides, and a genetic selection system to enrich correctly assembled full-length synthetic ORFs. The process is robust and scalable, enabling the parallel synthesis of closely related protein variants for applications in protein engineering and design.
Flow Cytometry Training talks - part 1
This forms the first session of the Garvan Flow , Flow Cytometry Training course. this is a 1 1/2 day training course aimed at giving new and experienced researchers a better understanding of cytometry in medical and biological research.
GIAB Integrating multiple technologies to form benchmark SVs 180517GenomeInABottle
Genome in a Bottle aims to provide well-characterized human genomes as benchmarks to validate genome sequencing and variant calling. The summary characterizes five genomes that have been analyzed to provide benchmark calls for simple and some complex variants, though many challenges remain, particularly for structural variants and difficult genomic regions. Integration of multiple data types and analyses from diverse technologies is key to improving benchmark calls over time in an open and transparent manner.
1. George Papadatos presented on mining compounds, targets, and indications from the patent corpus using SureChEMBL and Open PHACTS.
2. He outlined how SureChEMBL annotates chemicals in patents and links them to biological data for Open PHACTS, and how relevance scoring helps prioritize important entities.
3. Examples were given of using the Open PHACTS API and patent data in SureChEMBL for use cases like identifying key compounds, analyzing chemical spaces, and integrating external data.
1
Phylogenetic Analysis Homework assignment
This assignment will be completed on your own and turned in the week of 11/8-11/10.
Introduction
Molecular evolution is the study of how proteins and nucleic acids evolve. Included in this
field are studies of mutations and chromosomal rearrangements, the evolutionary process,
the identification of sequence patterns conferring function in proteins and nucleic acids,
and the reconstruction of the evolutionary history of organisms and the molecules that
they make. All of these studies rely on comparisons of nucleotide or amino acid sequences.
In this tutorial, you will be introduced to some of the fundamental principles of molecular
evolution and the types of bioinformatics tools that are used in evolutionary studies. We
will begin by carrying out a manual sequence comparison, so that the basic concepts can
be introduced, and the remainder of the project will be carried out at The Biology
Workbench, a set of bioinformatics analysis programs managed by The San Diego
Supercomputing Center at the University of California, San Diego.
Objectives
• To introduce the principles of molecular evolution
• To acquaint you with the tools that are available to compare nucleotide and
amino acid sequences
• To learn about the use of protein sequences in reconstructions of evolutionary history
Project
Branching evolution occurs when one ancestral species gives rise to two or more progeny
species. However, speciation events don't involve the vast majority of the genes in a
genome. That is, for most genes, both of the progeny species inherit identical genes from
the ancestor. Following speciation, these genes evolve independently in the separate
lineages. Studies of molecular evolution therefore rely heavily on comparisons of related
sequences from different organisms.
Shown below is an alignment of two homologous sequences that we will use as a starting
place. Homologous sequences are sequences that have descended from a common
ancestral sequence. You can't meaningfully compare sequences unless they are
homologous. This alignment uses the single letter amino acid code, in which G represents
glycine, Q represents glutamine, etc. The aligned proteins have been shown to be involved
in the metabolism of similar, but different, toxic compounds. As you can see, these amino
acid sequences are very similar and it is easy to recognize that they are related by common
descent.
2
dntAc: KMGVDDEVIVSRQNDGSVR
nahAc: KMGIDDEVIVSRQSDGSIR
An expanded version of this alignment is shown below. In this expanded alignment, both
the amino acids and the corresponding DNA nucleotides are shown. For ease of analysis,
the codons have been broken into separate entries in a table.
Alignment of nahAc and dntAc sequences.
K M G V D E V I V
dntAc AAA ATG GGC GTC GAT GAA GTC ATC GTC
nahAc ...
This document discusses techniques for analyzing gene expression in formalin-fixed paraffin-embedded (FFPE) tissue samples using real-time PCR. FFPE samples are valuable for biomarker studies but RNA extracted from them is fragmented and damaged. The document presents a new method called RT2 FFPE PreAMP technology that combines improved RNA extraction and reverse transcription with a preamplification step to enhance detection of genes from FFPE samples in real-time PCR analysis. It allows for multi-gene expression profiling from archived clinical samples. Testing showed the method improved detection of genes and increased the positive call rate to 100% compared to standard methods.
Bioinformatic tools analyze biological sequences to find similarities, domains, and coding regions. BLAST is a widely used tool that compares a query sequence to database sequences to find regions of similarity, helping scientists determine sequence function. Sequence alignment identifies similar character patterns between two or more sequences and can provide information about function, structure, and evolutionary relationships. CpG islands are regions of DNA where cytosine and guanine nucleotides frequently occur next to each other. Methylation of cytosines within CpG islands can regulate gene expression and is an epigenetic mechanism studied in cancer diagnosis.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cel...Qiagen - Egypt
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
Cell-based Reporter Assays: Measure 45 Signaling Pathway Activity in Any Cell...QIAGEN
Would you like to measure signaling pathway activity in your favorite cell? Learn how to successfully apply convenient and robust reporter assays to your RNA interference, gene over-expression, protein, or small molecule studies. The Cignal Reporter Assays are an excellent tool for studying pathway signaling activity in cells that are amenable to transfection, available for studying numerous pathways including (ROS, Wnt, NF-kB, Notch, cAMP/PKA, TGFbeta, and the Cignal Lenti Reporter Assays combines the power of a lentiviral delivery system with our robust transcription factor reporter technology, enabling you to study signal pathways in virtually any cell type. You can find a technology overview, protocol tutorial, and application examples in the following presentation.
This document provides instructions for experiments involving bioinformatics tools and software. It begins with introductory information and a table of contents. The experiments cover topics like downloading sequences from NCBI, performing BLAST searches, converting between protein and nucleotide sequences, downloading and using MEGA and other software for phylogenetic analysis, primer design, sequence cleaning and formatting, and more. Step-by-step instructions are provided for completing each analysis using various online and offline bioinformatics resources.
This document provides an overview of protein sequence analysis techniques. It discusses using databases like UniProt to search unknown protein sequences and analyze BLAST search results. It also describes tools for predicting protein structure and function from sequence, including secondary structure prediction, homology modeling, and multiple sequence alignments to identify evolutionary relationships between proteins. The goal of protein sequence analysis is to characterize proteins in silico and infer their potential structure and function based on sequence similarity and evolutionary relationships to other known proteins.
I. The document outlines a proteogenomics course at EMBL-EBI, discussing integrating proteomics and genomics data.
II. It discusses what proteogenomics is, using multi-omics approaches to correlate genomic and proteomic sequence events like mutations and modifications.
III. The talk will cover integrating proteomics data into Ensembl and UCSC trackhubs, as well as tools for proteogenomics analysis.
Similar to IB Chemistry on ICT, Protein Sequencing , Chimera, Jmol, Pymol for Internal Assessment on Hemoglobin, Myoglobin and Cytochrome (20)
IA on efficiency of immobilized enzyme amylase (yeast extract) in alginate be...Lawrence kok
Sodium alginate reacts with calcium chloride to form calcium alginate beads that can immobilize enzymes like amylase from yeast extract. These beads were added to a solution of starch and iodine, which produces a blue-black color. As the immobilized amylase breaks down the starch into maltose and simple sugars over 3 minutes, the blue-black color fades. The rate of starch hydrolysis was measured by the decrease in absorbance of the blue-black color over time using a colorimeter.
IA on effect of duration on efficiency of immobilized MnO2 in alginate beads ...Lawrence kok
Sodium alginate and calcium chloride were used to immobilize MnO2 catalyst particles in alginate beads. MnO2-loaded beads were prepared using 3% sodium alginate and 2% calcium chloride solutions and tested in the decomposition of hydrogen peroxide over 4 days. The rate of reaction and efficiency decreased slightly each day, from an initial rate of 0.1976 kPas-1 and 100% efficiency on day 1 to 0.1528 kPas-1 and 77% efficiency on day 4, demonstrating the durability of the immobilized MnO2 catalyst beads over multiple reuse cycles.
IA on effect of concentration of sodium alginate and calcium chloride in maki...Lawrence kok
The document investigates the effect of sodium alginate and calcium chloride concentration on forming alginate beads. Various concentrations of sodium alginate (1%, 2%, 3%) and calcium chloride (1%, 2%, 3%) were used to form beads. 3% sodium alginate added to 2% calcium chloride produced the strongest, biggest beads. This combination will be used to immobilize the catalyst MnO2 in alginate beads so that it can be reused instead of being discarded after reaction with H2O2.
IA on effect of duration (steeping time) on polyphenol (tannins) of tea, usin...Lawrence kok
This document examines the effect of steeping time on the polyphenol content of green tea, as measured by potassium permanganate titration. Green tea bags were steeped in a water bath at 90C for durations ranging from 1 to 5 minutes. The polyphenol content was found to increase linearly with steeping time, ranging from 1247 mg/L after 1 minute to 2078 mg/L after 5 minutes. The titration procedure involved adding tea steeped for different times to a solution with an indicator, and titrating with potassium permanganate solution until the endpoint was reached.
IA on polyphenol quantification using potassium permanganate titration (Lowen...Lawrence kok
This document describes the quantification of polyphenols using potassium permanganate titration. Some key points:
1. Polyphenols are antioxidants found in fruits like grapes, berries, and cider that can be quantified using a redox titration with potassium permanganate.
2. The procedure involves preparing a 0.004M potassium permanganate solution and titrating fruit extracts with it using indigo carmine as an indicator, until the solution turns greenish yellow at the endpoint.
3. The volume of permanganate used corresponds to the amount of polyphenols present, with green grapes containing the most at 665 mg/L tannic acid equivalents based on the titration
Main Java[All of the Base Concepts}.docxadhitya5119
This is part 1 of my Java Learning Journey. This Contains Custom methods, classes, constructors, packages, multithreading , try- catch block, finally block and more.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
আমাদের সবার জন্য খুব খুব গুরুত্বপূর্ণ একটি বই ..বিসিএস, ব্যাংক, ইউনিভার্সিটি ভর্তি ও যে কোন প্রতিযোগিতা মূলক পরীক্ষার জন্য এর খুব ইম্পরট্যান্ট একটি বিষয় ...তাছাড়া বাংলাদেশের সাম্প্রতিক যে কোন ডাটা বা তথ্য এই বইতে পাবেন ...
তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
বিসিএস ও ব্যাংক এর লিখিত পরীক্ষা ...+এছাড়া মাধ্যমিক ও উচ্চমাধ্যমিকের স্টুডেন্টদের জন্য অনেক কাজে আসবে ...
How to Build a Module in Odoo 17 Using the Scaffold MethodCeline George
Odoo provides an option for creating a module by using a single line command. By using this command the user can make a whole structure of a module. It is very easy for a beginner to make a module. There is no need to make each file manually. This slide will show how to create a module using the scaffold method.
This presentation was provided by Steph Pollock of The American Psychological Association’s Journals Program, and Damita Snow, of The American Society of Civil Engineers (ASCE), for the initial session of NISO's 2024 Training Series "DEIA in the Scholarly Landscape." Session One: 'Setting Expectations: a DEIA Primer,' was held June 6, 2024.
This presentation includes basic of PCOS their pathology and treatment and also Ayurveda correlation of PCOS and Ayurvedic line of treatment mentioned in classics.
Assessment and Planning in Educational technology.pptxKavitha Krishnan
In an education system, it is understood that assessment is only for the students, but on the other hand, the Assessment of teachers is also an important aspect of the education system that ensures teachers are providing high-quality instruction to students. The assessment process can be used to provide feedback and support for professional development, to inform decisions about teacher retention or promotion, or to evaluate teacher effectiveness for accountability purposes.
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Thinking of getting a dog? Be aware that breeds like Pit Bulls, Rottweilers, and German Shepherds can be loyal and dangerous. Proper training and socialization are crucial to preventing aggressive behaviors. Ensure safety by understanding their needs and always supervising interactions. Stay safe, and enjoy your furry friends!
The simplified electron and muon model, Oscillating Spacetime: The Foundation...RitikBhardwaj56
Discover the Simplified Electron and Muon Model: A New Wave-Based Approach to Understanding Particles delves into a groundbreaking theory that presents electrons and muons as rotating soliton waves within oscillating spacetime. Geared towards students, researchers, and science buffs, this book breaks down complex ideas into simple explanations. It covers topics such as electron waves, temporal dynamics, and the implications of this model on particle physics. With clear illustrations and easy-to-follow explanations, readers will gain a new outlook on the universe's fundamental nature.
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
RPMS TEMPLATE FOR SCHOOL YEAR 2023-2024 FOR TEACHER 1 TO TEACHER 3
IB Chemistry on ICT, Protein Sequencing , Chimera, Jmol, Pymol for Internal Assessment on Hemoglobin, Myoglobin and Cytochrome
1. Electrostatic Potential (ESP)
Measure polarization
Electron Map density
Electron distribution
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 3D model
Click here download Rasmol
Click here download PyMolClick here download Jmol
Click here Chem EDDL
Click here chemical search.Click here CRC database
Modelling and 3D representation
Chemistry Database
Click here Spectra database(OhioState) Click here Spectra database (NIST)
Click here chem finder.
Spectroscopic Database
Click here down Swiss PDB
Modelling and 3D representation
Click here crystallography database.
✓ ✓
Click here NIST data
✓Click here download Arguslab
Click here chem axon
Click here download Avagrado
Click here chem EdDL
Click here download chimera
✓
2. Measure polarization
Electron Map density
Electron distribution
Electrostatic Potential (ESP)
Dipole Moment
Measure bond length/angle
Measure bond strength
Organic softwarefor 3D model
Click here download Rasmol
Click here download PyMolClick here download Jmol
Click here Chem EDDL
Click here chemical search.
Modelling and 3D representation
Quick Chemistry DatabaseCheck
Click here down Swiss PDB
Modelling and 3D representation
✓ ✓
Click here NIST data
✓Click here download Arguslab
Click here chemaxon quick chem check
Click here download Avagrado
Click here chem EdDL
Click here for Visualization/3D sources
Click here download Marvin Sketch
Click here quick chemical check
Click here quick chemical check
3. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 4HHB
Click here Chimera tutorial
1
2
Uses molecular modelling
1
2
Chemicalviewer 3D structure(Chimera)
Download PDB text file
File – fetch by ID- 4HHB
Select – residue – HEM
Select – chain A – Action – Ribbon – Hide
Select – chain B,C,D - Action – ribbon Hide
Display only ligand Heme
Tool- structural analysis - Distance
Select 2 atom
-by press control/shift/left click select 2 points
Tool – structure analysis – create to get distance
3
Check here 4HHB Chimera 1MBO
Select Histidine that are close to ring
Locate His F8 and E7
Make measurement
Click here download chimera
Tool – Sequence – choose sequence for 4 chains
Identify amino acids of interest
4
4. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 4HHB and 1NEJ
1
2 Uses molecular modelling
1
Sequence comparison bet Hemoglobin vs Sickle Cell
File – fetch by ID- 4HHB (Normal) and 1NEJ (Sickle)
Tool – Structural comparison – Match maker
3
Click here download chimera
Match – 4HHB (normal) with 1NEJ (Sickle) Both align/overlap together
4
Tool – Structural comparison – Match Align
5
match align
5. Match Align bet 4HHB chain A with 1NEJ chain A
6 7 sequence
comparison
8
Info – Percentage identity
Compare 4HHB chain A with 1NEJ chain A
Result – 97.8% identical
9
10
Click here Chimera tutorial
Click here Chimera sequence comparison
Check here 4HHB Chimera 1MBO
Compare 4HHB chain B with 1NEJ chain B
Result – 98.6% identical
Mutation of
amino acid 6 - Valine
9
10
Sequence comparison bet Hemoglobin vs Sickle Cell
6. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 2B4Z and 1HRC
1
2 Uses molecular modelling
1
File – fetch by ID- 2B4Z and 1HRC
Tool – Structural comparison – Match maker
3
Click here download chimera
Match – 2B4Z (Bovine) with 1HRC (Horse) Both align/overlap together
4
Tool – Structural comparison – Match Align
5
match align
Sequence comparison - Cytochrome2B4Z (bovine) with 1HRC (horse)
7. Match Align bet 2B4Z (bovine) with 1HRC (horse)
6 7 sequence
comparison
8
Info – Percentage identity
Compare 2B4Z (bovine) with 1HRC (horse)
Result – 97.1% identical
910
Click here Chimera tutorial
Click here Chimera sequence comparison
Check here 4HHB Chimera 1MBO
Sequence comparison - Cytochrome2B4Z (bovine) with 1HRC (horse)
Tools – Sequence – Blast Protein
(find similar protein sequence)
8. Sequence comparison - Cytochrome2B4Z (bovine) with other organism
Click here NCBI
1
Enter protein pdb – 2B4Z – Run Blast (Alignment)
List of organism with similar protein sequence
Check here NCBI Blast video
Alignment – Check organism to compare
– Multiple alignment
Click here download chimera
Tools – Sequence – Blast Protein – 2B4Z
(find similar protein sequence)
1
Result – 97.1% identical
2 2
3 3
Click here Clustal Omega
Paste protein sequence from NCBI (notepad)
that are similar to 2B4Z
Paste sequence to Clustal Omega
Press submit
1
2
Result of organism matching 2B4Z protein
9. Type PDB code – 4HHB
Right click – select Hetero
Select - HETATM – HEM
4 Heme is display from 4 chains
Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Click here J mol protein video
Chemical viewer 3D structure (Jmol)
Uses molecular modelling
1
J mol executable file
Measure distance
Select measure – distance for porphyrin ring
Measure ring size/distance Fe from plane
Select protein – by residue – Histidine
Measure and locate His F8
Measure and locate His E7
final heme – click here
J mol executable file
1
Type 4HHB into protein data bank
Look for ligand Heme
Model kit to
design molecule
Click here deoxyhemoglobin chimera
2
2
3
4
3
4
final product
All histidine shown
Get structure from
PDB and MOL
10. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Organic softwarefor 3D model (Pymol)
1 1
Click here - Protein Data Bank
Protein database key in - PDB 4 letter code
3
Click here download PyMol
Click here Pymol video tutorial
Click file – open your download pdb file
from Protein Data bank
Get to command term – Type fetch 4HHB
H - Hide – S - Show cartoon – C – Type by ss
Select 4 Hem – Look for 4 Hemes
Select 4HHB – H – hide everything
Select Heme – Show stick
Look His – select and name His F8 and His E7
2
Press S – sequence at bottom screen.
Right click – zoom in
Select HEM - hemoglobin
4
Uses molecular modelling
2
Select heme – right click – action – around 5A
Look for His F8 and E7 around heme
Make measure for distance
Double click to display name of atom
11. Measure bond length/angle
Measure number H2 bonds
Measure bond strength
Protein 1, 2 , 3O structure
Presence of disulfide bond
Presence alpha and beta pleated sheet
Protein Data Bank
Protein database key in - PDB 4HHB
Click here Swiss PDB tutorial
1
2
Uses molecular modelling
1
2
Chemicalviewer 3D structure(Swiss PDB)
Download PDB text file
File – open 4HHB pdb downloaded from databank
Window – Control panel
Remove – side chain
Select – Group kind – HETATM
Display – stereo view
Show only selected 4 Heme
Click here down Swiss PDB
Select – Group kind – Histidine
Select – Residue – close to 2A
Locate Histidine and make measurement
3
Check for heme and Histidine
only from control panel
Select Histidine that are close to ring
Locate His F8 and E7 and make measurement
4
13. Possible ResearchQuestion
Measuring using 3D modelling and Sequencing Technique
Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NCBI
Click here UCSC
Click here Ensembl
Myoglobin Hemoglobin Cytochrome
Hemoglobin Chimera Pymol Jmol Swiss PDB Mean
Orientation His/Fe Similar Similar Similar Similar Similar
Bond length N - Fe 2.12A 1.90A 2.02A 2.02A 2.01A
Bond length Fe – E7 5.93A 5.80A 5.45A 5.42A 5.55A
Bond length Fe – F8 2.25A 2.05A 2.10A 2.21A 2.13A
Chimera Swiss PDB
Myoglobin Chimera Pymol Jmol Swiss PDB Mean
Orientation His/Fe Similar Similar Similar Similar Similar
Bond length N - Fe 2.02A 2.11A 2.15A 2.32 2.14A
Bond length Fe – E7 5.80A 5.71A 5.56A 5.25A 5.25A
Bond length Fe – F8 2.15A 2.25A 2.11A 2.21A 2.21A
His E7
Fe
N
His F8
- Structuraland sequence similarity for Hemo/Myo and cytochromeamong
various species
- Is His E7/F8 orientation similar for Hemoglobin, Myoglobin, Cytochrome
- Is there any differencesbet distance/position/orientationof porphyrin ring for
Hemoglobin, Myoglobin, Cytochrome
- How is Fe2+located, along or out of plane for Hemo/Myoglobin/Cytochrome
- Is distancebet Fe and ligand N of porphyrin the same for
Hemoglobin/Myoglobin/Cytochrome
- Investigate the conserved domain/regionsin Hemo/Myo and Cytochrome that
are needed to ensure survival of species
- Why His E7 and F8 are locatedin such a way across many different species? Is
their orientation highly conserved and why?
- Sequence similarity among cytochromesfound in diff species of organism
Structuraland Sequencesimilarity for Hemo/Myoglobin and Cytochrome
Sequence similarity bet
Hemoglobin and Myoglobin
Structuralsimilar of
Heme group
Result – 97.8% identical
14. Possible ResearchQuestion Data Collection using 3D modelling
Data Collection using Database
Click here Jmol Click here PyMol
Click here NCBI
Click here UCSC
Click here Ensembl
Myoglobin Hemoglobin Cytochrome
Chimera Swiss PDB
- Structuraland sequence similarity for Hemo/Myo and cytochromeamong
various species
- Is His E7/F8 orientation similar for Hemoglobin, Myoglobin, Cytochrome
- Is there any differencesbet distance/position/orientationof porphyrin ring for
Hemoglobin, Myoglobin, Cytochrome
- How is Fe2+located, along or out of plane for Hemo/Myoglobin/Cytochrome
- Is distancebet Fe and ligand N of porphyrin the same for
Hemoglobin/Myoglobin/Cytochrome
- Investigate the conserved domain/regionsin Hemo/Myo and Cytochrome that
are needed to ensure survival of species
- Why His E7 and F8 are locatedin such a way across many different species? Is
their orientation highly conserved and why?
- Sequence similarity among cytochromesfound in diff species of organism
Structuraland Sequencesimilarity for Hemo/Myoglobin and Cytochrome
Evaluationand Limitationusing 3D modelling
Must use a variety of sources/programme to verify/validate the validity and reliability of data collected
Average is computed from diff software and checked with database to confirm.
Check on methodological limitation using 3D model. (MUST perform 3D Optimization to most stable form structure.
Critical and skeptical of result produced by computational chemistry.
Major limitation of computation, they assume non-interacting molecule. (Ideal situation, ex molecule in vacuum or isolated state)
Most appropriate molecule are those whose coordinates are not theoretical but derive from experimental structural determination
(using X ray diffraction)
Be careful of predicted arrangement from simulation /3D model
Data sources are supported using diff method/3D model/database
Certain database like NIST and CRC are more reliable source
Check if there is a good agreement bet CRC, diff databases and 3D model prediction before making conclusion
Computation programme is always based on approximation and we cannot conclusive prove anything
Reflect of validity and reliability of data
Is model a true representation of reality?
15. - Porphyrin gp of heterocyclic made of 4 pyrrole subunit
- Porphyrin macrocyclehas 26 (delocalized) pi electron, obey Hückel rule
- It is aromatic,4n+2 π. (Highly conjugated system)
Heme
PorphyrinHeme = Fe + porphyrins ring
Heme
Heme A Heme B Heme C
Mitochondria
- cytochromec oxidase
- electrontransport
O2
Heme = Fe + porphyrin ring – carry O2
Fe2+ located
Most abundant
Hemoglobin and Myoglobin
Mitochondria
- cytochromec
- electrontransport
Fetal Hemoglobin
(2α22γ2)
Human Hemoglobin
(2α2 2β2)
Sickle cell Hemoglobin
(2α22βS
2)
Myoglobin
1 α chain
16. Heme
Heme A Heme B Heme C
Mitochondria
- cytochromec oxidase
- electrontransport
Most abundant
Hemoglobin and Myoglobin
Mitochondria
- cytochromec
- electrontransport
Fetal Hemoglobin
(2α22γ2)
Human Hemoglobin
(2α2 2β2)
Sickle cell Hemo
(2α22βS
2)
Myoglobin
1 α chain
Cytochrome
Heme in cytochrome,highly conjugated ring sys surrounding Fe
Cytochrome- REDOX rxn – mitochondria – ATP/energy productionvia elec transport chain
Many type cytochromes – Cyto a, b, c1, a3
Cytochromec, an ancient protein, developed early in the evolution of life. Essential protein for energy/ATP
HIGHLY CONSERVED has changed little in millions of years.
Many variation – but structureremain relatively unchanged
Fe in cytochrome Fe in cytochrome Cytochromec – heme c
17. Hemoglobin A - 2 alpha and 2 beta chains
Hemoglobin A2 - 2 alpha and 2 delta chains
Hemoglobin F - 2 alpha and 2 gamma chainsHeme (porphyrin) bind to Fe2+using 4 nitrogen atom (histidine gp) Porphyrin
- as electron-pair donor - polydentate ligand
Fe form 2 additional bonds, one on each side of the heme plane.
These binding sites call fifth and sixth coordination sites.
This hisitidine is referred as proximal Histidine F8
The sixth coordination site bind oxygen with His E7 nearby
Deoxyhemoglobin
Fe2+- out plane
Can’t fit the ring
Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe2+
Heme
(porphyrin)
Oxyhemoglobin
Fe2+- located in plane
Fit the ring
Deoxyhemoglobin
Fe2+ out plane
Can’t fit the ring
Out by 0.06nm
Fe2+ in plane
Fit the ring
Human hemoglobin - 2 alpha chain - 144 amino acid
- 2 beta chain - 146 amino acid
Fe bind to six ligand. 4 with N atom of porphyrin
Fifth ligand is donated by His F8
O2 add to Fe as sixth ligand
O2 tilt relative to perpendicular of heme plane
His F8His F8 His F8
His E7
His E7
His E7
Oxyhemoglobin
18. Heme
Hemoglobin - 4 chain - 4 heme (porphyrin) - 4 Fe 2+
Fe2+
Heme
(porphyrin)
Hemoglobin - 2 alpha chain - 144 amino acid
- 2 beta chain - 146 amino acid
Fe bind to six ligand. 4 with N atom of porphyrin
Fifth ligand is donated by His F8
O2 add to Fe as sixth ligand
O2 tilt relative to perpendicularof heme plane
His E7 locateover Fe, force CO to bind to Fe at an angle.
This steric hinderance reduce afinity of CO in hemoglobin.
O2 bind to Fe at an angle, its binding not affected
by presence of His E7.
His (E7)
His (F8)
vs
Myoglobin - 1 chain – 1 heme (porphyrin) - 1 Fe2+
- 154 amino acids
HemoglobinMyoglobin
Fe2+
Heme
(porphyrin)
His (F8)
His (E7)