Structure database: PDB Tuomas Hätinen. Protein Data Bank A repository for 3-D biological macromolecular structure. It includes proteins, nucleic acids.

Slides:

Advertisements

Similar presentations

Publisher perspective eBank/R4L/SPECTRa Joint Consultation Workshop London Metropole Hotel 20 October 2006.

Advertisements

Protein Structure.

Worldwide Protein Data Bank Worldwide Protein Data Bank  Formalization of current working practice  Members  RCSB (Research.

Dictionaries and Ontologies in Structural Biology.

Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik.

Swiss-Prot Protein Database Daniel Amoruso December 2, 2004 BI 420.

Archives and Information Retrieval

Protein structure determination. Tertiary protein structure: protein folding Three main approaches: [1] experimental determination (X-ray crystallography,

Protein Structure, Databases and Structural Alignment

Workshop on Biological Macromolecular Structure Models RCSB Protein Data Bank Rutgers, The State University of New Jersey.

Journals.iucr.org/f/ Acta Crystallographica Section F Structural Biology and Crystallization Communications An electronic journal for macromolecular structure.

Computing for Bioinformatics Lecture 8: protein folding.

High Throughput Processing of the Structural Information of the Protein Data Bank Zoltán Szabadka, Vince Grolmusz Department of Computer Science Eötvös.

Management and Distribution of Chemical Data in the Protein Data Bank John Westbrook, Dimitris Dimitropoulos, Jasmine Young, Peter Rose, Philip E. Bourne.

Pharm201 Lecture Data Representation Pharm 201/Bioinformatics I Philip E. Bourne Department of Pharmacology, UCSD Prerequisite Reading: Structural.

Structure Representation and Coordinates Format Lecture 3 Structural Bioinformatics Dr. Avraham Samson

Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik.

Worldwide Protein Data Bank Worldwide Protein Data Bank Agenda  Welcome and Introductions  Overview of recent wwPDB progress.

Number of released entries Year. Growth of Molecular Complexity Number of Chains Year Number of Structures Containing that Number of Chains.

Part II : Introduction To Protein Structure Kong Lesheng Victor Tong Joo Chuan National University of Singapore.

Development of Bioinformatics and its application on Biotechnology

Erice 2008 Introduction to PDB Workshop From Molecules to Medicine: Integrating Crystallography in Drug Discovery Erice, 29 May - 8 June Peter Rose

23 rd August 2005CCP4 Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and PDB Deposition Tools IUCr.

Evaluation of Structure Quality Using RCSB PDB Tools Kyle Burkhardt, Lead Data Annotator The RCSB PDB at Rutgers University.

X-ray crystallography NMR cryoEM Experimental approaches for structural biology.

Introduction to databases Tuomas Hätinen. Topics File Formats Databases -Primary structure: UniProt -Tertiary structure: PDB Database integration system.

23 rd August 2005CCP4-RCSB Workshop IUCr 2005 Florence Italy 1 N6: A Protein Crystallographic Toolbox: The CCP4 Software Suite and RCSB PDB Deposition.

SMART Teams: Students Modeling A Research Topic Jmol Training 101!

Gene Annotation and Analysis Lab Work Reference: European Multimedia Bioinformatics Educational Resource.

MEDG421 MediaWiki Create & Edit a Wiki Page Stefanie Butland

Helen M. Berman, Rutgers University EMBO Practical Course Section: Searching Structure Databases September 26, 2008 PSI Structural Genomics Knowledgebase.

Macromolecular Visualization or… Where to go when ChemDraw just isn’t enough Martin Case Chem

Worldwide Protein Data Bank Worldwide Protein Data Bank History of the PDB  1970s  Community discussions about how to establish.

EBI is an Outstation of the European Molecular Biology Laboratory. Annotation Procedures for Structural Data Deposited in the PDBe at EBI.

Crystallographic Databases I590 Spring 2005 Based in part on slides from John C. Huffman.

MolIDE2: Homology Modeling Of Protein Oligomers And Complexes Qiang Wang, Qifang Xu, Guoli Wang, and Roland L. Dunbrack, Jr. Fox Chase Cancer Center Philadelphia,

REMINDERS 2 nd Exam on Nov.17 Coverage: Central Dogma of DNA Replication Transcription Translation Cell structure and function Recombinant DNA technology.

Data Integration and Management A PDB Perspective.

Module 3 Protein Structure Database/Structure Analysis Learning objectives Understand how information is stored in PDB Learn how to read a PDB flat file.

Protein Tertiary Structure. Protein Data Bank (PDB) Contains all known 3D structural data of large biological molecules, mostly proteins and nucleic acids:

Biochemistry - as science; biomolecules; metabolic ways. Structure of proteins, methods of its determination.

Protein Data Bank: An Introduction Learning to Use the RCSB PDB Portal.

EBI is an Outstation of the European Molecular Biology Laboratory. Quaternary Structure.

Pharm201 Lecture Data Representation Pharm 201/Bioinformatics I Philip E. Bourne Department of Pharmacology, UCSD Prerequisite Reading: Structural.

Data Harvesting: automatic extraction of information necessary for the deposition of structures from protein crystallography Martyn Winn CCP4, Daresbury.

EBI is an Outstation of the European Molecular Biology Laboratory. Sanchayita Sen, Ph.D. PDB Depositions Validation & Structure Quality.

A MULTIBODY ATOMIC STATISTICAL POTENTIAL FOR PREDICTING ENZYME-INHIBITOR BINDING ENERGY Majid Masso Laboratory for Structural Bioinformatics,

EBI is an Outstation of the European Molecular Biology Laboratory. Protein Database in Europe Deposition, Validation, Search and Analysis Services.

Real World Experiences in Operating a Collaboratory: The Protein Data Bank Helen M. Berman Board of Governors Professor of Chemistry.

Primary vs. Secondary Databases Primary databases are repositories of “raw” data. These are also referred to as archival databases. -This is one of the.

EBI is an Outstation of the European Molecular Biology Laboratory. PDBeChem The Ligand Database.

Lecture 10 CS566 Fall Structural Bioinformatics Motivation Concepts Structure Solving Structure Comparison Structure Prediction Modeling Structural.

Dr. Abdelkrim Rachedi. 1. General introduction to bioinformatics. 2. Databases in biology: -> 2.1. Databases for the primary structure of Proteins and.

Building an Invisible Puzzle: Predicting Protein Structure and Function from Sequence Matthew Perella January 31, 2013.

Afternoon session: The archival problem and infrastructure for solutions Prof John R Helliwell Interactive Publications.

PDBe Protein Interfaces, Surfaces and Assemblies

Introduction to RCSB PDB Data, Tools and Resources

Application of Tabular Data Model to explore and analyze the

Getting the Most out of the PDBe

Archives and Information Retrieval

Protein 3d structure Our understanding of life at the molecular level is highly dependent on the ability to map the molecular details of individual proteins.

Jmol Training Session Part I: Introduction to the Protein Data Bank

Structural biology Our understanding of life at the molecular level is highly dependent on the ability to map the molecular details of individual proteins.

Number of released entries

CCP4-PDB Workshop ACA 2004 Chicago

Introduction to Databases

The site to download BALBES:

Crystal structure description

SUBMITTED BY: DEEPTI SHARMA BIOLOGICAL DATABASE AND SEQUENCE ANALYSIS.

Presentation transcript:

Structure database: PDB Tuomas Hätinen

Protein Data Bank A repository for 3-D biological macromolecular structure. It includes proteins, nucleic acids and viruses. Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%).

Protein Data Bank Founded in 1971 by Brookhaven National Laboratory, New York. Transferred to the Research Collaboratory for Structural Bioinformatics (RCSB) in Currently it holds 40,000 released structures.

Protein Data Bank

PDB data formats PDB file format was used to contain the coordinates and related information. In the late 1990 ’ s, macromolecular Crystallographic Information file (mmCIF) evolved. mmCIF and PDBML Push in to make structure files completely self-contained descriptions of the experiment and details of the structure determination. PDB file format unstructured and obsolete

PDB File Format Text file – you can edit with a text editor e.g. WordPad Atomic co-ordinates Rich annotation Citation Experimental Method Biological source e. Etc.

Demo & Exercises