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

Slides:

Advertisements

Similar presentations

Data Curation in Crystallography: Publisher Perspectives JISC Data Cluster Consultation Workshop CCLRC, Didcot, Oxon 10 October 2006.

Advertisements

Protein Structure.

SG KB 2009 NIGMS Workshop: Enabling Technologies for Structural Biology Section on Structural Analysis Margaret J. Gabanyi March 4, 2009 How to Use the.

PSI Structural Genomics Knowledgebase Helen M. Berman Bottlenecks Workshop April 14, 2008.

Lecture №2 State System of Scientific and Technical Information.

Nucleic Acid Database By Pooja Awatramani. Database Utilities Provides structural references in the form of base pair annotation for DNA, RNA, and some.

Protein Structure Database Introduction Database of Comparative Protein Structure Models ModBase 生資所 g 詹濠先.

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics USC School of Medicine Library.

Data Management in the DOE Genomics:GTL Program Janet Jacobsen and Adam Arkin Lawrence Berkeley National Laboratory University of California, Berkeley.

Workshop on Biological Macromolecular Structure Models RCSB PDB Piscataway, NJ November 19-20, 2005 Topic 3: Structural Genomics and Models Contributors:

EMDB Richard Newman Monica Chagoyen Mohamed Tagari EMBL-EBI Cryo-Electron Microscopy Structure Deposition Workshop RCSB Protein Data Bank in Rutgers University,

Using ArrayExpress. ArrayExpress is an international public repository for well-annotated microarray data, including gene expression, comparative genomic.

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

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.

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

Bringing Structure to Biology: Small Molecules and the PDBe

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.

CCP-EM community meeting 7 February 2013 EMDB and beyond Ardan Patwardhan and Gerard Kleywegt Protein Data Bank in Europe EMBL-EBI.

Network Services for Biologists in the Genome Era The Work of the European Bioinformatics Institute.

Protein 3D-structure analysis Exercises. Practicals Find update frequency for RCSB PDB: weekly. When was the last update? How many protein structures.

Retention and preservation within the Copac Tools Michael Emly University of Leeds CCM Workshop 19 March 2012.

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

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

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

Adding GO for Large Datasets COST Functional Modeling Workshop April, Helsinki.

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

Biological Databases Biology outside the lab. Why do we need Bioinfomatics? Over the past few decades, major advances in the field of molecular biology,

Copyright OpenHelix. No use or reproduction without express written consent1.

The Functional Genomics Experiment Object Model (FuGE) Andrew Jones, School of Computer Science, University of Manchester MGED Society.

Alastair Kerr, Ph.D. WTCCB Bioinformatics Core An introduction to DNA and Protein Sequence Databases.

Workshop on Structural and Computational Proteomics of Biological Complexes.

Data Integration and Management A PDB Perspective.

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

Biological databases Exercises. Discovery of distinct sequence databases using ensembl.

Workshop on Biological Macromolecular Structure Models RCSB PDB Piscataway, NJ November 19-20, 2005 Topic 4: Current Database Resources and Models Contributors:

Protein Sequence Analysis - Overview - NIH Proteomics Workshop 2007 Raja Mazumder Scientific Coordinator, PIR Research Assistant Professor, Department.

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

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

3D-EM DAS Extending DAS to 3D-EM and Fitting /02/26.

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

Macromolecular Structure Database Project EMSD Infra-structure Services for Europe To develop an autonomous structural database capability in Europe

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

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

EM Maps and Models in EMDB/PDB. Growth of EM entries

EBI is an Outstation of the European Molecular Biology Laboratory. UniProtKB Sandra Orchard.

Discussion Summary for the Challenge Wah Chiu

Bioinformatics Project BB201 Metabolism A.Nasser

Copyright OpenHelix. No use or reproduction without express written consent1.

SG KB 2009 NIGMS Workshop: Enabling Technologies for Structural Biology Section on Structural Analysis Helen M. Berman March 4, 2009 How to use the PSI.

The Bovine Genome Database Abstract The Bovine Genome Database (BGD, facilitates the integration of bovine genomic data. BGD is.

Homology 3D modeling Miguel Andrade Mainz, Germany Faculty of Biology,

PDBe Protein Interfaces, Surfaces and Assemblies

Take a REST from manual searching: PDBe, programmatically

Introduction to RCSB PDB Data, Tools and Resources

Using ArrayExpress.

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

The Protein Data Bank: Evolution of a key resource in biology

Number of released entries

Presentation Title Here

Predicting Active Site Residue Annotations in the Pfam Database

Background: Currently CCP4i puts each structure determination into a separate project directory, and automatically keeps a “Project History Database” recording.

TargetDB and PEPCDB •

Finding databases by subject

The site to download BALBES:

Volume 26, Issue 6, Pages e2 (June 2018)

SUBMITTED BY: DEEPTI SHARMA BIOLOGICAL DATABASE AND SEQUENCE ANALYSIS.

Presentation transcript:

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

Models in the PDB  Ambiguous policies over the years  Revisit decision to remove models

The Ambiguities  Define line between “pure” models and models based on data  Large experimental spectrum e.g. X- ray, NMR, EM, SAX, FRET models  Homology models especially as derived from structural genomics  Need a way to archive models that is totally compatible with PDB

Background  Models moved to separate directory on FTP site July 1, 2002  981 models in archives to date  Models can be search by PDB ID and using a search form specific to models (via ID, author, and title)

981 Released Models YearHPUBHOLDOBSRELWAITPROC WDRN Total < Total

Questions  What are the needs of the modeling community with respect to the archiving of models?  What are the needs of the experimentalists with respect to the availability of models? What are the current limitations of theoretically derived models?  How could the scientific community at large be best served with respect to the availability and annotation of models?  What measures, if any, should be used to assess the quality of models?

Topics Topic 1: Summary of types of theoretical models (Discussion Leader: Andrej Sali) Topic 2: Electron microscopy and models (Discussion Leader: Wah Chiu) Topic 3: Structural genomics and models (Discussion Leader: Stephen K. Burley) Topic 4: Current database resources and models (Discussion Leader: Torsten Schwede)