Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
Some good references on the subject:
The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time.
A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results.
Chou-Fasman algorithm is an empirical algorithm developed for the prediction of protein secondary structure
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time.
A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results.
Chou-Fasman algorithm is an empirical algorithm developed for the prediction of protein secondary structure
This presentation gives you a detailed information about the swiss prot database that comes under UniProtKB. It also covers TrEMBL: a computer annotated supplement to Swiss-Prot.
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Ab Initio Protein Structure Prediction is a method to determine the tertiary structure of protein in the absence of experimentally solved structure of a similar/homologous protein. This method builds protein structure guided by energy function.
I had prepared this presentation for an internal project during my masters degree course.
Open reading frame is part of reading frame that contains no stop codons or region of amino acids coding triple codons.
ORF starts with start codon and ends at stop codon.
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. This presentation deals with what, why, how, where and who of PDB. In this presentation we have also included briefing about various file formats available in PDB with emphasis on PDB file format
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Ab Initio Protein Structure Prediction is a method to determine the tertiary structure of protein in the absence of experimentally solved structure of a similar/homologous protein. This method builds protein structure guided by energy function.
I had prepared this presentation for an internal project during my masters degree course.
Open reading frame is part of reading frame that contains no stop codons or region of amino acids coding triple codons.
ORF starts with start codon and ends at stop codon.
Prediction of the three dimensional structure of a given protein sequence i.e. target protein from the amino acid sequence of a homologous (template) protein for which an X-ray or NMR structure is available based on an alignment to one or more known protein structures
Global and local alignment (bioinformatics)Pritom Chaki
A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
Describes the structural organisation of proteins with example and its determination, interrelationship b/w structure and function of proteins, also biologically important peptides is covered.
by Dr. N. Sivaranjani, MD
20.1 Characteristics of Proteins
20.2 Amino Acids: The Building Blocks for Proteins
20.3 Essential Amino Acids
20.4 Chirality and Amino Acids
20.5 Acid–Base Properties of Amino Acids
20.6 Cysteine: A Chemically Unique Amino Acid
20.7 Peptides
20.8 Biochemically Important Small Peptides
20.9 General Structural Characteristics of Proteins
20.10 Primary Structure of Proteins
20.11 Secondary Structure of Proteins
20.12 Tertiary Structure of Proteins
20.13 Quaternary Structure of Proteins
20.14 Protein Hydrolysis
20.15 Protein Denaturation
20.16 Protein Classification Based on Shape
20.17 Protein Classification Based on Function
20.18 Glycoproteins
20.19 Lipoproteins
Top 5 Deep Learning and AI Stories - October 6, 2017NVIDIA
Read this week's top 5 news updates in deep learning and AI: Gartner predicts top 10 strategic technology trends for 2018; Oracle adds GPU Accelerated Computing to Oracle Cloud Infrastructure; chemistry and physics Nobel Prizes are awarded to teams supported by GPUs; MIT uses deep learning to help guide decisions in ICU; and portfolio management firms are using AI to seek alpha.
Protein Structural Prediction
1. Molecular Structure prediction
2. Sequence
3. Protein Folding
4. The Leventhal Paradox
5. Energy (Minimization )
6. The Hydrophobic Effect
7. Protein Structure Determination ( X-ray,NMR)
8. Ab initio Prediction
9. Lattice String Folding
10. Rosetta (Monte Carlo based method)
11. Homology-based Prediction
Hemoglobin estimation and Blood typing experiment and Vijay Hemmadi
A hemoglobin test measures the amount of hemoglobin in your blood. Hemoglobin is a protein in your red blood cells that carries oxygen to your body's organs and tissues and transports carbon dioxide from your organs and tissues back to your
The ABO group consists of four possibilities: A, B, AB, and O. The Rh type is either positive or negative. Individuals with AB Positive blood are known as universal recipients because they can receive any one of the blood groups or Rh types in a blood transfusion
Determination of protein concentration by Bradford method.pptxVijay Hemmadi
Bradford uses Coomasie Blue which is a dye that binds specifically to proteins. It is very accurate and sensitive, compatible with most buffers, sugars, and chaotropic agents but high concentrations of detergent interfere in the assay
Mining is the extraction of valuable minerals or other geological materials from the earth from an orebody, lode, vein, seam, reef or placer deposits which forms the mineralized package of economic interest to the miner.
Ores recovered by mining include metals, coal, oil shale, gemstones, limestone, dimension stone, rock salt, potash, gravel, and clay. Mining is required to obtain any material that cannot be grown through agricultural processes, or created artificially in a laboratory or factory. Mining in a wider sense includes extraction of any non-renewable resource such as petroleum, natural gas, or even water.
Laboratory method for measuring enzyme activity.
Vital for study of enzyme kinetics and enzyme inhibition.
Measurement of enzyme activity – follow the change in concentration of substrate or product – measure reaction rate.
Liposomes-Classification, methods of preparation and application Vijay Hemmadi
liposome preparation and application
A liposome is a tiny bubble (vesicle), made out of the same material as a cell membrane. Liposomes can be filled with drugs, and used to deliver drugs for cancer and other diseases. Membranes are usually made of phospholipids, which are molecules that have a head group and a tail group
A natural disaster is the effect of earths natural hazards, for example flood, tornado, hurricane, volcanic eruption, earthquake, heatwave, or landslide. They can lead to financial, environmental or human losses. The resulting loss depends on the vulnerability of the affected population to resist the hazard, also called their resilience. If these disasters continue it would be a great danger for the earth
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
if your doing fish dissection and need some anatomical information then go through my slides.
in this i have written fish anatomy with its physiological implications
Are you looking for some good journals to publish your data? Then this is the correct time to read my article. I am writing this with the hope of inhibiting you from publishing your data in predatory and fake journals.
These are the following criteria you should know before submitting your manuscript to a journal:
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
2. INRODUCTION
Primary structure (Amino acid sequence)
↓
Secondary structure (α-helix, β-sheet)
↓
Tertiary structure (Three-dimensional
structure formed by assembly of secondary
structures)
↓
Quaternary structure (Structure formed by
more than one polypeptide chains)
3. Secondary Structure
Defined as the local conformation of protein backbone
Primary Structure —folding— Secondary Structure
a helix and b sheet
Secondary Structure
Regular Secondary
Structure
(a-helices, b-sheets)
Irregular
Secondary
Structure
(Tight turns,
Random coils,
bulges)
4.
5. a helix
•common confirmation.
•spiral structure
•Tightly packed coiled polypeptide
backbone, with extending side chains
•Spontaneous
•stabilized by H-bonding between amide
hydrogens and carbonyl oxygens of peptide
bonds.
•R-groups lie on the exterior of the helix
and perpendicular to its axis.
•complete turn of helix —3.6 aminoacyl
residues with distance 0.54 nm
e.g. the keratins- entirely α-helical
Myoglobin- 80% helical
6. •Glycine and Proline , bulky amino acids,
charged amino acids favor disruption of the
helix.
7. b sheet
•β-sheets are composed of 2 or more different regions of
stretches of at least 5-10 amino acids.
•The folding and alignment of stretches of the polypeptide
backbone aside one another to form β-sheets is stabilized by
H-bonding between amide hydrogens and carbonyl oxygens
•the peptide backbone of the β sheet is highly extended.
•R groups of adjacent residues point in opposite directions.
• β-sheets are either parallel or antiparallel
10. What is secondary
structure prediction?
Given a protein sequence (primary structure)
1st step in prediction of protein structure.
Technique concerned with determination of secondary structure of
given polypeptide by locating the Coils Alpha Helix Beta Strands in
plypeptide
GHWIATRGQLIREAYEDYRHFSSECPFIP
Predict its secondary structure content
(C=Coils H=Alpha Helix E=Beta Strands)
CEEEEECHHHHHHHHHHHCCCHHCCCCCC
11. Why secondary structure
prediction?
o secondary structure —tertiary structure prediction
o Protein function prediction
o Protein classification
o Predicting structural change
o detection and alignment of remote homology between proteins
o on detecting transmembrane regions, solvent-accessibleresidues,
and other important features of molecules
o Detection of hydrophobic region and hydrophilic region
12. Prediction methods
o Statistical method
o Chou-Fasman method, GOR I-IV
o Nearest neighbors
o NNSSP, SSPAL
o Neural network
o PHD, Psi-Pred, J-Pred
o Support vector machine (SVM)
o HMM
13. Chou-Fasman algorithm
Chou and fasman in 1978
It is based on assigning a set of prediction value to amino
acid residue in polypeptide and applying an algorithm to the
conformational parameter and positional frequency.
conformational parameter for each amino acid is calculated
by considering the relative frequency of each 20 amino
acid in proteins
By this C=Coils H=Alpha Helix E=Beta Strands are
determined
Also called preference parameter
14. • A table of prediction value or preference parameter for each
of 20 amino acid in alpha helix ,beta plate and turn
already calculated and standardised.
• To obtain the prediction value the frequency of amino
acids( i) in structure is divided by of all residences in
protein (s)
• i/s
• The resulting structural parameter of
p(alpha),p(beta),p(turn)vary —0.5 to 1.5 for 20 amino acid
15.
16. Window is scanned to find a short sequence of
amino acid that has high probability to form one
type of structure
When 4 out of 6 amino acid have high
probability >1.03 the – alpha helix
3 out of 5 amino acid with probability >1.03-beta
RULES
17. ALGORITHM
o Note preference parameter for 20 aa in peptide
o Scan the window and identify the region where 4 out of
6 contiguous residue have p(alpha helix) >1.00
o Continue scanning in both the direction until the 4
contiguous residue that have an average p(alpha
helix)<1.00,end of helix
o If segment is longer than 5aa and p(alpha helix)>p(beta
sheet )-segment –completely alpha helix
o scan different segment and identify - alpha helix
18. Identify the region where 3 out of 5 aa have the
value of p( beta sheet) >1.00 ,region is predicted
as beta sheet
Continue scanning both the direction until 4
residue that have p( beta sheet) <1.00
End of beta sheet
average p( beta sheet) >105 and p( beta sheet)
>p(alpha helix) than consider complete segment
as b pleated sheet
19. If any region is over lapping than consider it as
alpha helix if average p(alpha helix)>p(beta sheet )
Or beta sheet if p(alpha helix)<p(beta sheet )
To identify turn
P(t)=f(j)f(j+1)f(j+2)f(j+3)
J=residual number
23. GOR METHOD
• GOR(Garnier,Osguthorpe,Robson)1978
• Chou fasman method is based on assumption that each amino
acid individually influence the 2ry structure of sequence
• GOR is based on, amino acid flanking the central amino acid
will influence the 2ry structure
• Consider a peptide central amino acid
side amino acid
• It assume that amino acid up to 8 residue on sides will
influence the 2ry structure of central residue
• 4th version
• 64% accurate
24. ALGORITHUM
•It uses the sliding window of 17 amino acid
•The side amino acid sequence and alignment is determined to
predict secondary structure of central sequence
•Good for helix than sheet because beta sheet has more inter
sequence hydrogen bonding
•36.5% accurate for beta sheet
•input any amino acid sequence
•Output tells about secondary structure
25.
26. NEAREST NEIGHBOUR
METHOD
o Based on ,short homologues sequences of amino acids
have the same secondary structure
o It predicts secondary structure of central homologues
segment by neighbour homologues sequences
o By using structural database find some secondary
structure of sequence which may be homologues to our
target sequence
o Naturally evolved proteins with 35% identical amino acid
sequence will have same secondary structure
o Find some sequence which may match with target
sequence
o Scoring matrix,MSA
30. Neural network
Input signals are summed
and turned into zero or one
3.
J1
J2
J3
J4
Feed-forward multilayer network
Input layer Hidden layer Output layer
neurons
37. Suggested reading:
Chapter 15 in “Current Topics in Computational Molecular
Biology, edited by Tao Jiang, Ying Xu, and Michael Zhang. MIT
Press. 2002.”
Bioinformatics by Cynthia and per jambeck
Bioinformatics by S.C.RASTOGI
Bioinformatics By Andreas
Optional reading:
Review by Burkhard Rost:
http://cubic.bioc.columbia.edu/papers/2003_r
ev_dekker/paper.html
Reference