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
INTRODUCTION.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
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.
INTRODUCTION.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
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 DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
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.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC.
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.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
BITS: Overview of important biological databases beyond sequencesBITS
Module 4 Other relevant biological data sources beyond sequences
Part of training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
Protein Sequence, Structure, and Functional Databases: UniProtKB, Swiss-Prot, TrEMBL, PIR, MIPS, PROSITE, PRINTS, BLOCKS, Pfam, NDRB, OWL, PDB, SCOP, CATH, NDB, PQS, SYSTERS, and Motif. Presented at UGC Sponsored National Workshop on Bioinformatics and Sequence Analysis conducted by Nesamony Memorial Christian College, Marthandam on 9th and 10th October, 2017 by Prof. T. Ashok Kumar
Lecture delivered by T. Ashok Kumar, Head, Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil, Thuckalay, INDIA. UGC Sponsored National Workshop on BIOINFORMATICS AND GENOME ANALYSIS for College Teachers on August 11 & 12, 2014. Organized by Centre for Bioinformatics, Department of Zoology, NMCC.
"A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. A simple database might be a single file containing many records, each of which includes the same set of information."
Composite: It compile and filter sequence data from primary database.
Specialized : database—allows targeted searching on one or more specific subject areas
Broadly, plant tissue culture refers to “in vitro cultivation of all plant parts, whether a single cell, a tissue or an organ under aseptic conditions”. This is a technique with which “the plant cells, tissues or organs are on an artificial nutrient medium, either static or liquid, under aseptic and controlled conditions”.This presentation includes the requirements of PTC, various techniques of PTC
Probability distribution is a way to shape the sample data to make predictions and draw conclusions about an entire population because most improvement projects and scientific research studies are conducted with sample data rather than with data from an entire population. Probability distribution helps finding all the possible values a random variable can take between the minimum and maximum possible values
Regression analysis is a powerful statistical method that allows you to examine the relationship between two or more variables of interest. Regression analysis is a reliable method of identifying which variables have impact on a topic of interest. The process of performing a regression allows you to confidently determine which factors matter most, which factors can be ignored, and how these factors influence each other.In this presentation a brief introduction about SLR and MLR and their codes in R are described
Chemistry Development Kit is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. In this presentation a brief history of CDK, the various facilities provided by it, it's applications, and various analytical tools based on CDK such as CDK-Taverna, Bioclipse, PaDEL, Cinfony and, CDK extensions exist for KNIME are discussed.
Validation is the process of checking that your model is consistent with stereochemical standards i.e., validation is the process of evaluating reliability
In this presentation various aspects of validation are discussed
Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms .The metabolome is the global collection of all low molecular weight metabolites that are produced by cells during metabolism, and provides a direct functional readout of cellular activity and physiological status. In this presentation i have given the list of various Metabolomic databases and metabolite databases. In addition to this there is a brief description about SMPDB and HMDB and BioTransformer
PHARMACOGNOSTICAL AND BIOLOGICAL ACTIVITY EVALUATION OF DECALEPIS HAMILTONIIAlichy Sowmya
Man requires basic necessities i.e. food, shelter and cloth. In addition to this attempts were made to reduce the severity of the disease or to cure different ailments. The biodiversity of natural resources like plants, animals, microbes, minerals and marine sources has served this need since time immemorial. Plants have played a crucial role in maintaining human health and improving the quality of human life for thousands of years. The World Health Organization has estimated that 80% of the earth’s inhabitants rely on traditional medicine for their health care needs, and most of this therapy involves the use of plants extracts or their active components.The use of the plants as medicine has been followed traditionally as trial and error and the effect of the plant medicine is being passed from generation to generation. It is orally familiar to the rustics.The plant is traditionally found to be useful for many ailments like haemorrhage, thirst,antimicrobial, urticaria, jaundice, gout, blood disorders and for diabetes. The literature review revealed that antibacterial activity was reported for leaves and roots of Decalepis aryalpathra.The genus Decalepis has been reported to posses different classes of compound mainly tannin,saponin, carbohydrate, fatty acid, flavanoids, alkaloids etc, which are responsible for antimicrobial and anthelmintic activity and also for treatment of various diseases.However, there is no scientific evidence to verify these claims. There is a dearth of reports on
pharmacognostical, antimicrobial and anthelminthic activity of Decalepis hamiltonii. In view of the above, the current study was designed to verify these indigenous claims and to provide basis for the rationale use of tuberous herb namely Decalepis hamiltonii (D. hamiltonii,Asclepiadaceae), as antimicrobial and antihelminthic drug.
SciFinder and its utility in Drug discoveryAlichy Sowmya
SciFinder Scholar® is a Z39.50 Windows-based interface that provides easy access to the rich and diverse scientific information contained in the CAS databases including Chemical Abstracts from 1907 onwards. SFS is an elegant search interface to six core chemical-related databases. Five of these databases are produced by CAS itself
Prescription Filling Record is the record of the original prescription and refill records. In this report, the various contents of the record , the procedures for dispensing the records and the procedures for the storage of the records have been discussed.
Information science is a multi disciplinary science with applications in a wide range of aspects. In this presentation there is a brief introduction to what is information science, how it orginated and characteristics of information science. It also covers the various definitions of information science.
Limitations of in silico drug discovery methodsAlichy Sowmya
In drug discovery there are various in silico approaches such as Virtual high throughput screening, Molecular docking, Homology modelling, QSAR, CoMFA, Molecular Dynamics, and Pharmacophore mapping. In this presentation various limitations of these approaches are given
Crimean Congo Hemorrhagic fever is a deadly infection of CCHFV. CCHFV is a biosafety level 4 virus. In this presentation the general introduction to the CCHF and CCHFV is given along with various computational drug design approaches for CCHF
New Drug Discovery and Development .....NEHA GUPTA
The "New Drug Discovery and Development" process involves the identification, design, testing, and manufacturing of novel pharmaceutical compounds with the aim of introducing new and improved treatments for various medical conditions. This comprehensive endeavor encompasses various stages, including target identification, preclinical studies, clinical trials, regulatory approval, and post-market surveillance. It involves multidisciplinary collaboration among scientists, researchers, clinicians, regulatory experts, and pharmaceutical companies to bring innovative therapies to market and address unmet medical needs.
These simplified slides by Dr. Sidra Arshad present an overview of the non-respiratory functions of the respiratory tract.
Learning objectives:
1. Enlist the non-respiratory functions of the respiratory tract
2. Briefly explain how these functions are carried out
3. Discuss the significance of dead space
4. Differentiate between minute ventilation and alveolar ventilation
5. Describe the cough and sneeze reflexes
Study Resources:
1. Chapter 39, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 34, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 17, Human Physiology by Lauralee Sherwood, 9th edition
4. Non-respiratory functions of the lungs https://academic.oup.com/bjaed/article/13/3/98/278874
NVBDCP.pptx Nation vector borne disease control programSapna Thakur
NVBDCP was launched in 2003-2004 . Vector-Borne Disease: Disease that results from an infection transmitted to humans and other animals by blood-feeding arthropods, such as mosquitoes, ticks, and fleas. Examples of vector-borne diseases include Dengue fever, West Nile Virus, Lyme disease, and malaria.
Pulmonary Thromboembolism - etilogy, types, medical- Surgical and nursing man...VarunMahajani
Disruption of blood supply to lung alveoli due to blockage of one or more pulmonary blood vessels is called as Pulmonary thromboembolism. In this presentation we will discuss its causes, types and its management in depth.
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Ethanol (CH3CH2OH), or beverage alcohol, is a two-carbon alcohol
that is rapidly distributed in the body and brain. Ethanol alters many
neurochemical systems and has rewarding and addictive properties. It
is the oldest recreational drug and likely contributes to more morbidity,
mortality, and public health costs than all illicit drugs combined. The
5th edition of the Diagnostic and Statistical Manual of Mental Disorders
(DSM-5) integrates alcohol abuse and alcohol dependence into a single
disorder called alcohol use disorder (AUD), with mild, moderate,
and severe subclassifications (American Psychiatric Association, 2013).
In the DSM-5, all types of substance abuse and dependence have been
combined into a single substance use disorder (SUD) on a continuum
from mild to severe. A diagnosis of AUD requires that at least two of
the 11 DSM-5 behaviors be present within a 12-month period (mild
AUD: 2–3 criteria; moderate AUD: 4–5 criteria; severe AUD: 6–11 criteria).
The four main behavioral effects of AUD are impaired control over
drinking, negative social consequences, risky use, and altered physiological
effects (tolerance, withdrawal). This chapter presents an overview
of the prevalence and harmful consequences of AUD in the U.S.,
the systemic nature of the disease, neurocircuitry and stages of AUD,
comorbidities, fetal alcohol spectrum disorders, genetic risk factors, and
pharmacotherapies for AUD.
TEST BANK for Operations Management, 14th Edition by William J. Stevenson, Ve...kevinkariuki227
TEST BANK for Operations Management, 14th Edition by William J. Stevenson, Verified Chapters 1 - 19, Complete Newest Version.pdf
TEST BANK for Operations Management, 14th Edition by William J. Stevenson, Verified Chapters 1 - 19, Complete Newest Version.pdf
Report Back from SGO 2024: What’s the Latest in Cervical Cancer?bkling
Are you curious about what’s new in cervical cancer research or unsure what the findings mean? Join Dr. Emily Ko, a gynecologic oncologist at Penn Medicine, to learn about the latest updates from the Society of Gynecologic Oncology (SGO) 2024 Annual Meeting on Women’s Cancer. Dr. Ko will discuss what the research presented at the conference means for you and answer your questions about the new developments.
Lung Cancer: Artificial Intelligence, Synergetics, Complex System Analysis, S...Oleg Kshivets
RESULTS: Overall life span (LS) was 2252.1±1742.5 days and cumulative 5-year survival (5YS) reached 73.2%, 10 years – 64.8%, 20 years – 42.5%. 513 LCP lived more than 5 years (LS=3124.6±1525.6 days), 148 LCP – more than 10 years (LS=5054.4±1504.1 days).199 LCP died because of LC (LS=562.7±374.5 days). 5YS of LCP after bi/lobectomies was significantly superior in comparison with LCP after pneumonectomies (78.1% vs.63.7%, P=0.00001 by log-rank test). AT significantly improved 5YS (66.3% vs. 34.8%) (P=0.00000 by log-rank test) only for LCP with N1-2. Cox modeling displayed that 5YS of LCP significantly depended on: phase transition (PT) early-invasive LC in terms of synergetics, PT N0—N12, cell ratio factors (ratio between cancer cells- CC and blood cells subpopulations), G1-3, histology, glucose, AT, blood cell circuit, prothrombin index, heparin tolerance, recalcification time (P=0.000-0.038). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and PT early-invasive LC (rank=1), PT N0—N12 (rank=2), thrombocytes/CC (3), erythrocytes/CC (4), eosinophils/CC (5), healthy cells/CC (6), lymphocytes/CC (7), segmented neutrophils/CC (8), stick neutrophils/CC (9), monocytes/CC (10); leucocytes/CC (11). Correct prediction of 5YS was 100% by neural networks computing (area under ROC curve=1.0; error=0.0).
CONCLUSIONS: 5YS of LCP after radical procedures significantly depended on: 1) PT early-invasive cancer; 2) PT N0--N12; 3) cell ratio factors; 4) blood cell circuit; 5) biochemical factors; 6) hemostasis system; 7) AT; 8) LC characteristics; 9) LC cell dynamics; 10) surgery type: lobectomy/pneumonectomy; 11) anthropometric data. Optimal diagnosis and treatment strategies for LC are: 1) screening and early detection of LC; 2) availability of experienced thoracic surgeons because of complexity of radical procedures; 3) aggressive en block surgery and adequate lymph node dissection for completeness; 4) precise prediction; 5) adjuvant chemoimmunoradiotherapy for LCP with unfavorable prognosis.
Explore natural remedies for syphilis treatment in Singapore. Discover alternative therapies, herbal remedies, and lifestyle changes that may complement conventional treatments. Learn about holistic approaches to managing syphilis symptoms and supporting overall health.
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
Dr. Vidisha Kumari, a leading epidemiologist in Bangalore, emphasizes the importance of getting vaccinated. "The flu vaccine is our best defense against the influenza virus. It not only protects individuals but also helps prevent the spread of the virus in our communities," he says.
This year, the flu season is expected to coincide with a potential increase in other respiratory illnesses. The Karnataka Health Department has launched an awareness campaign highlighting the significance of flu vaccinations. They have set up multiple vaccination centers across Bangalore, making it convenient for residents to receive their shots.
To encourage widespread vaccination, the government is also collaborating with local schools, workplaces, and community centers to facilitate vaccination drives. Special attention is being given to ensuring that the vaccine is accessible to all, including marginalized communities who may have limited access to healthcare.
Residents are reminded that the flu vaccine is safe and effective. Common side effects are mild and may include soreness at the injection site, mild fever, or muscle aches. These side effects are generally short-lived and far less severe than the flu itself.
Healthcare providers are also stressing the importance of continuing COVID-19 precautions. Wearing masks, practicing good hand hygiene, and maintaining social distancing are still crucial, especially in crowded places.
Protect yourself and your loved ones by getting vaccinated. Together, we can help keep Bangalore healthy and safe this flu season. For more information on vaccination centers and schedules, residents can visit the Karnataka Health Department’s official website or follow their social media pages.
Stay informed, stay safe, and get your flu shot today!
3. • The Protein Data Bank (PDB) is a database for the three-dimensional structural data
of large biological molecules, such as proteins and nucleic acids
• The data, typically obtained by X-ray crystallography, NMR spectroscopy, or,
increasingly, cryo-electron microscopy
• The data is freely accessible on the Internet via the websites of its member
organizations (PDBe, PDBj, RCSB, and BMRB)
• The PDB is overseen by an organization called the Worldwide Protein Data Bank,
wwPDB
What is PDB ?
4. Why did it start ?
Growing
crystallographic
data
Development of
BRAD in 1968
5. • In 1969, Dr Edgar Meyer began to write software to store atomic coordinates files in
a common format to make them available for geometric and graphical evaluation
(with sponsorship of Dr. Walton Hamilton at Bookhaven National laboratory
• In 1971, one of Dr. Meyer’s programs – SEARCH, enabled networking, that enabled
the researches to access information from database to study protein structures offline
• In 1973, upon Hamilton’s death, Dr. Tom Koetzle took over direction of PDB fo 20
years
How did it start ?
6. • In 1980s, IUCr guidelines established, number of structures deposited increases and
independent biological databases such as the NDB were established
• In Oct, 1998, PDB was transferred to Research Collaboratory for Structural
Bioinformatics (RCSB), complete transfer since 1999. Dr. Helen M Berman of
Rutgers University was the new director
• In 2003, with the formation of wwPDB, the PDB became an international
organization having three member organizations
• In 2006, the BMRB joined PDB
How did it start ?
7. Who runs it ?
The Worldwide PDB
(wwPDB) organization
manages the PDB archive and
ensures that the PDB is freely
and publicly available to the
global community
Protein Data Bank
in Europe
Protein Data Bank
Japan
Research Collaboratory for Structural
Bioinformatics Protein Data Bank
Biological Magnetic Resonance
Data Bank
8. Who runs it ?
Rich information about all PDB entries,
multiple search and browse facilities,
advanced services including PDBePISA,
PDBeFold and PDBeMotif, advanced
visualisation and validation of NMR and EM
structures, tools for bioinformaticians
9. Who runs it ?
Supports browsing in multiple languages
such as Japanese, Chinese, and Korean;
SeSAW identifies functionally or
evolutionarily conserved motifs by
locating and annotating sequence and
structural similarities, tools for
bioinformaticians, and more
10. Who runs it ?
Simple and advanced searching for
macromolecules and ligands, tabular
reports, specialized visualization tools,
sequence-structure comparisons,
RCSB PDB Mobile, Molecule of the
Month and other educational resources
at PDB-101, and more
11. Who runs it ?
Collects NMR data from any experiment and
captures assigned chemical shifts, coupling
constants, and peak lists for a variety of
macromolecules; contains derived annotations
such as hydrogen exchange rates, pKa values,
and relaxation parameters
17. • The PDB is a repository of atomic coordinates and other information describing
proteins and other important biological macromolecules
• Structural biologists use methods such as X-ray crystallography, NMR spectroscopy,
and cryo-electron microscopy to determine the location of each atom relative to each
other in the molecule
• They then deposit this information, which is then annotated and publicly released into
the archive by the wwPDB
How data is collected?
18. • RCSB PDB website, allow you to search and explore the information under the PDB
header, including information on experimental methods and the chemistry and
biology of the protein
• Once you have found the PDB entries that you are interested in, you may
use visualization programs to allow you to read in the PDB file, display the protein
structure on your computer, download the information and create custom pictures of
it
• These programs also often include analysis tools that allow you to measure distances
and bond angles, and identify interesting structural features
How to retrieve the data ?
19. • One can search for their protein of interest by using the search bar in the RCSB PDB
website
• It allows one to search either by typing the PDB ID, name of the author (who has
deposited the structure), or the sequence of the protein or any particular ligand of
interest
How to search ?
20. • PDB ID, is the 4-character unique identifier of every entry in the Protein Data Bank
• A 4-character PDB ID is assigned to each new structure at the time of deposition
• The first character is a numeral in the range 1-9, while the last three characters can be
either numerals (in the range 0-9) or letters (in the range A-Z)
• If the PDB ID of an entry in the Protein Data Bank is known, it is the most direct way
to retrieve it from the database
• However, this can’t be used as an identifier for biomolecules, because several
structures of the same molecule in different enviroments or different conformations
are contained in PDB with different PDB IDs
PDB ID
21. • One or more PDB IDs can be typed or copied and pasted in the search box. Multiple
IDs can be separated by commas or white space, including line breaks.
• Example:
Enter 4HHB into the text box next to "PDB ID(s)" and press "Submit Query". The Structure Summary page
for 4HHB will load
Enter 2HHB, 3HHB, 4HHB into the text box and press "Submit Query". A Query Results Browser page with
a brief summary of the three structures will load. From there, clicking a PDB ID, thumbnail image, or
structure title will load the Structure Summary page for the respective ID
PDB ID
23. • The data in PDB is usually stored in 3 different file formats
PDB file format
mmCIF format
PDBML
File formats
24. • mmCIF is the acronym for the macromolecular Crystallographic Information File
• mmCIF is based on a subset of the syntax rules for the Self Defining Text Archive
(STAR) file
• A Dictionary Description Language (DDL) defines the structure of mmCIF
dictionaries
• Dictionaries provide the metadata which define the content of mmCIF data files
• mmCIF data files, dictionaries and DDLs all are expressed in a common syntax
mmCIF
25. • The Protein Data Bank Markup Language (PDBML) provides a representation of
PDB data in XML format
• The description of this format is provided in XML schema of the PDB Exchange
Data Dictionary
• This schema is produced by direct translation of the PDBx/mmCIF Exchange Data
Dictionary Other data dictionaries used by the PDB have been electronically
translated into XML/XSD schemas
PDBML
26. • The Protein Data Bank Markup Language (PDBML) provides a representation of
PDB data in XML format
• The description of this format is provided in XML schema of the PDB Exchange
Data Dictionary
• This schema is produced by direct translation of the PDBx/mmCIF Exchange Data
Dictionary Other data dictionaries used by the PDB have been electronically
translated into XML/XSD schemas
PDB file format
27. How to read PDB file ?
• Sections of an Entry
The following table lists the various sections of a PDB coordinate entry and the
records comprising them:
28. How to read PDB file ?
• Types of Records
It is possible to group records into categories based upon how often the record type
appears in an entry.
Single:
There are records that may only appear one time (without continuations) in
a file. It is an error for a duplicate of any of these records to appear in an
entry.
Once in an entry but exceed the number of columns available:
There are records that conceptually exist only once in an entry, but the
information content may exceed the number of columns available. These
records are therefore continued on subsequent lines.
29. How to read PDB file ?
• Types of Records
Multiple:
Most record types appear multiple times, often in groups where the
information is not logically concatenated but is presented in the form of a list.
Many of these record types have a custom serialization that may be used not
only to order the records, but also to connect to other record types.
Multiple in an entry but exceed the number of columns available:
These records are therefore continued on subsequent lines. The second and
subsequent lines contain a continuation field which is a right-justified integer.
This number increments by one for each additional line of the record, and is
followed by a blank character.
30. How to read PDB file ?
• Types of Records
Grouping:
There are three record types used to group other records.
Other:
The remaining record types have a detailed inner structure.
31. How to read PDB file ?
• Types of Records
Single:
32. How to read PDB file ?
• Types of Records
Once in an entry but exceed the number of columns available :
33. How to read PDB file ?
• Types of Records
Multiple :
34. How to read PDB file ?
• Types of Records
Multiple in an entry but exceed the number of columns available :
35. How to read PDB file ?
• Types of Records
Grouping :
36. How to read PDB file ?
• Types of Records
Other :
JRNL - Literature citation that defines the coordinate set
REMARK - General remarks, some are structured and some are
free form
37. How to read PDB file ?
• Order of Records:
All records in a PDB coordinate entry must appear in a defined order. Mandatory
record types are present in all entries. When mandatory data are not provided, the
record name must appear in the entry with a NULL indicator. Optional items become
mandatory when certain conditions exist.
41. Want to learn further ?
PDB-101 is an online portal for teachers, students, and the general public to
promote exploration in the world of proteins and nucleic acids. Learning
about the diverse shapes and functions of these biological macromolecules
helps to understand all aspects of biomedicine and agriculture, from protein
synthesis to health and disease to biological energy.
( http://pdb101.rcsb.org/ )