Structural Genomics Consortiums

 

Structural databases and on-line programs:

• RCSB (PDB) Macromolecular Structures
• PDB SUM (alternative structural database w/ links; Janet Thornton)
• Molecules R Us (NIH)
• Image database of Biological Macromolecules (IMB Jena)
• NCBI Structural Biology
• Obsolete PDB entries
• Nucleic acids database
• Cambridge Crystallographic Database
• ReLiBase (Protein Ligand Database from PDB)
• Protein Side Chain Database
• The DALI Server (Search for structural homologues)
• Atomic Nonlocal Environment Assessment Structure Validation
• UCLA-DOE Structural and Molecular Biology Server
• Biological Macromolecule Crystallization Database
• Protein Topology Homepage (Janet Thornton)
• Protein Data Bank Structure Validation Server
• Crystallographic Twinning Analysis Server (Yeates, UCLA)
• WhatCheck analysis of PDB entries
• MATRAS (3D structure superposition and comparison)
• MOLSURFER (Generation of interface maps of a molecular complex)
  
• Protein Structure Prediction (EMBL)
• META PP (Single interface to structure prediction servers)
  
• RNA World Website (IMB Jena)
• ExPASy Molecular Biology Server
  

Structural Genomics Initiatives and Centers:

• New York Structural Genomics Consortium (Rockefeller, Einstein, Brookhaven et al.: E. coli)
• Joint Çenter for Structural Genomics (Bay Area, SSRL: C. elegans and T. maritima)
• Southern California Consortium (UCLA, Scripps, etc.: Mycobacterium tuberculosis)
• Berkeley Structural Genomics Center (Mycoplasma genitalium and Mycoplasma pneumoniae)
• Northeast Structural Genomics Consortium (Yale etc: Various Eukaryotic Targets)
• Midwest Center for Structural Genomics (Argonne, Northwestern, Wash. U. etc: Various prokaryotic targets)
• Northwest Structural Genomics Center (UK, Daresbury: Various prokaryotic targets)
• New Jersey Initiative in Structural Genomics (Rutgers, Princeton)
• Structural Genomics of Pathogenic Protozoa (University of Washington)
  

Molecular biology databases, sequence searches and alignments:
 

• Exhaustive Compendium of molecular biology databases (NEB)
• Intein Database (Rebase; New England Biolabs)
• Restriction enzyme database (REBASE; New England Biolabs)
• European Bioinformatics Institute (EBI)
• EMBL Molecular Biology Services
• NCBI BLAST Server
• TIGR Microbial Genomics Database
• GOBase: Organellar Genomes
• Similarity Search Engines (Proweb)
• Sanger Center for Molecular Biology
• Washington University Center for Genomics
• ClustalW Multiple Alignments Server (EBI)
• MultAlin (Multiple Alignments at Toulouse)
• Phylogenetics Resources (Berkeley)
• RNA Gene Arrays (Brown Lab, Stanford)
• Codon Usage Database

Software and programmers: 

• 
  
• Bill Scott's Crystallography for OSX Webpage
• 
  
• ARP/wARP
• CCP4
• CNS
  
• Denzo/HKL/ScalePack Home Page
• DOCK WWW Page
• Dockvision
• GRASP,DELPHI
• CHIMERA (UCSF; replaces MIDAS)
• MolScript Home Page
• O Home Page
• POVRAY
• Raster3D
• SHELX
• SOLVE
• TNT
• Uppsala Software Factory
• VMD
• XPLOR
• XtalView

Companies:
 

• Charles Supper Co.
• Fischer Chemicals
• Hampton Research
• Molecular Simulations, Inc. (Accelerys, Inc)
• Molecular Structure Corporation
• New England Biolabs
• Novagen
• Proteins Solutions, Inc. (Light Scattering)

Crystallography / Crystallographers:
 

• Crystallography 101
• CrystaLinks (UW)
• Kevin Cowtan's Book of Fourier
• Kevin Cowtan's Structure Factor Tutorial
• X-RayView (Rice University Tutorial)
• CrystaLinks - A Crystallographer's Miscellany
• International Union of Crystallographers
• Tom Blundell's Heavy Atom Databank
• Cryo-cooling according to Brandeis University
• Crystool: Generating personalized crystallization matrices
• Anomalous Scatterers (Ethan Merritt, U.W.)

• Compendium of synchrotron sources of the world
• Biosynch: Biomolecular Crystallography Beamlines Page
• Advanced Light Source Home Page (LBNL, Berkeley)
• ALS Beamlines
• APS (Argonne)
• NSLS (Brookhaven) Beamlines
  
• SSRL (Stanford)
• Advanced Photon Source (APS) Home Page
• MacCHESS Macromolecular Crystallography Beamline
• Daresbury SRS