Government Agencies

Public Agencies

Private Institutions

Societies and Organizations

Databases

  • DIP, Database of Interacting Proteins
  • GPCRDB, Molecular-Specific Information System for G Protein-Coupled Receptors
  • Membrane Proteins 3D, Membrane Proteins of Known 3D Structure
  • ModBase, Database of Comparative Models
  • MPtopo, Membrane Protein Topology Database
  • PDB, RCSB Protein Data Bank
  • PFAM, Database of protein domains and HMMs
  • PubMed, Public Medline
  • SCOP, Structural Classification of Proteins
  • SMART, Identification and annotation of genetically mobile domains
  • Structural Biology Software Database, Pointers to software packages useful in structural biology
  • SubtiList, Bacillus subtilis genome sequencing project
  • SWISS-PROT and TrEMBL, Protein Database

Manuals

  • ASGL, PostScript plots
  • AMBER, package to perform molecular dynamics
  • AutoDock, Docking of flexible ligands to proteins
  • CHARMM, package to perform molecular dynamics
  • DDD, GUI Debugger
  • Dock, Docking program
  • GAUSSIAN, quantum mechanics
  • Grace, Plotting program Manual, Tutorial, and FAQ
  • GRASP, Surfaces and electrostatic calculations
  • GRID, Determining energetically favorable binding sites on molecules of known structure
  • GROMACS, Package to perform molecular dynamics
  • HMMER, Hidden Markov Model Package
  • LIGPLOT, Create ligand interaccion postscript plots
  • NAMD, package to perform molecular dynamics
  • MODELLER, Comparative Modeling
  • PHYLIP, Package of programs for inferring phylogenies (evolutionary trees)
  • VMD, Molecular Visualization

Programming

Web Servers

  • 123D+, Protein Sequence -> Structure Threading
  • AD-ENM, Analysis of Dynamics of Elastic Networks
  • BLAST, Sequence Similarity Searches
  • CASTP, Identification and measurements of protein cavities
  • CAVER, Identification of pathways from buried cavities to the surface
  • ClustalW, Multiple Alignments & Phylogenetic Trees
  • kPROT, prediction of the angular orientation of transmembrane segments
  • MATRAS, Protein 3D Structure Comparison
  • MORPH, 2D or 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations
  • MPEX, Membrane Protein Explorer (Topology, Hydropathy Plots)
  • NOMAD-REF, Normal Mode Analysis
  • P2P, Prediction of Correlated Mutations
  • PDB to MultiGIF, Takes a 3D structure (PDB file) and generates an animated image
  • pG calculation, model evaluation using ProsaII Z-Score
  • PRODRG, create molecular topologies
  • ROBETTA, full-chain protein structure prediction server
  • SOSUI, Classification and Secondary Structure Prediction of Membrane Proteins
  • TMAP, Transmembrane region prediction
  • TMHMM, Prediction of transmembrane helices in proteins
  • @TOME Meta-server, Submission of an amino acid sequence to six remote servers dedicated to structural predictions and fold recognition