The Stoddard Lab
Interesting Links
Interesting Links
Structural Biology Links
| Structural biology databases and servers | Molecular Biology Databases |
| Software/Programmers | Companies |
| Crystallography | Synchrotrons/Beamlines |
| 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
- 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
