TargetDB and PEPCDB http://targetdb.pdb.org/ • target-help@rcsb.rutgers.edu.

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Presentation transcript:

TargetDB and PEPCDB http://targetdb.pdb.org/ • target-help@rcsb.rutgers.edu

Target Registration Database TargetDB • http://targetdb.pdb.org/ Targets downloadable in XML (~43,000 targets) Targets downloaded from 17 worldwide centers weekly Target search by: Sequence (FASTA), project target ID, project site, status (selected, cloned, expressed, … in PDB), update date, protein name, source organism Report output in HTML, FASTA, and XML Integrates PDB entry sequences (~53,000 sequences) Includes PDB pre-release sequence data Provides links to related project sequence databases Summary reports of target and project progress 3-Tier architecture (Apache/Tomcat/MySQL) 29

TargetDB - Search Options Project target ID Date of status change Protein and source names Report formats

TargetDB - Status Search Status codes

TargetDB - Site Search Site list

TargetDB - Content Options Sequence collections

TargetDB - Sequence Search and search criterion

TargetDB - HTML Report Links to project and sequence databases Link to PDB Structure Explorer report

TargetDB - Site Status Summaries

TargetDB - Site Status Summaries Project target ID Report period Project site

TargetDB - Site Status Reports Expand report to target list

TargetDB - Site Target Progress Reports

Protein Expression Purification and Crystallization Database PEPCDB Extends content of TargetDB with: status history, stop conditions, reusable text protocols (cloning, expression, purification, crystallization, and NMR), protocol extensions, contact information Today - prototype database and query interface with data from CESG and SESG loaded Extends TargetDB search with: stop status, protocol type, protocol identifier, and protocol text Report output in HTML, FASTA, and XML Integrates PDB entry and pre-release sequences Reports provide links to status history, related protocols, project, sequence and domain databases 3-Tier architecture (Apache/Tomcat/IBM DB2) 29

PEPCDB - Search Options

PEPCDB - Search Options Stop status options

PEPCDB - Search Options Protocol search options

PEPCDB - HTML Reports Link to status history Links to domain sites Links to project and sequence sites Links to protocol descriptions

PEPCDB - Status History Report

PEPCDB - Links to Domain Databases

PEPCDB - Links to Protocol Descriptions