Web Resources

• Experimental techniques
• Circular Dichroism Facility

• Kinemages - Richardson's lab

• Protein Science Kinemages - a collection of many kinemages.

• Branden and Tooze Kinemages - a collection of kinemages to accompany "Introduction to PROTEIN STRUCTURE" by Branden and Tooze

• Molecules R US - Form for PDB query - access to all structures in the PDB, Protein Data Bank. Note that this contains nucleic acid structures as well as proteins.

• SwissProt Protein Sequence Database

• The Protein Databank

• The Nucleic Acid Database

• Computational services at NCBI
  • PubMed - Medline database
  • Entrez - General database search
  • BLAST - Protein sequence alignment
  • VAST - Structure-structure comparison

• Computational Services at EMBL

• PHD - secondary structure prediction
• STRIDE - assignment of secondary structure given atomic coordinates
• Columbia University Bioinformatics Center

• The new home of PredictProtein
• Computational Services at the European Bioinformatics Institute

• Protein Sequence databases
• DALI: compares a given protein structure with other PDB structures
• FSSP: Fold classification
• Jpred: consensus protein secondary structure prediction
• PQS: protein quaternary structure file server
• CLUSTALW: multiple sequence alignment
• TOPS: Searching and determining protein topology
• Computational Services at the French NPSA

• Secondary structure prediction
• Multiple alignments
• Homology search
• Computational Services at UCLA

• Verify 3D : Evaluates the quality of a protein structure
• ERRAT : Evaluates the quality of a protein structure
• Fold Recognition server
• CATH : Protein structure classification

• SCOP : Protein structure classification

• PFAM : Database of protein families

• Chandonia - Protein secondary structure prediction

• SAM-T98 - Protein secondary structure predictions using Hidden Markov Models

• Protein Structure Prediction Center

• Computational Services at the Swiss Institute of Bioinformatics

• Swiss-model: Automated homology modeling
• Swiss-Prot and TrEMBL: Protein sequence databases
• PROSITE - Database of protein families and domains
• ETH Zurich Bioinformatics server

• RNA secondary structure prediction:

• Belozersky Institute
• Vienna RNA package
• FITness
• A review article on the subject
• ISREC Bioinformatics

• TMpred: Predicting transmembrane domains

• Computational Services at Scripps

• Noname: Secondary structure prediction

• Protein structure assessment

• ANOLEA: Knowledge-based energy
• PROCHECK: Check stereochemical quality of protein structures
• Prosa II:
• PROVE - Protein Volume Evaluation
• Verify 3D
• WHAT-CHECK
• Cambridge crystallography
• GRASS Interactive graphics from the Honig lab
• Warwick Bioinformatics group

• PSIPRED Server

• PSIPRES: Secondary structure prediction
• MEMSAT: Transmembrane topology prediction
• GenTHREADER: Fold recognition
• FASTA - sequence similarity search

• DOMO - database of aligned protein domains

• PRODOM - Protein domain database

• 3D-PSSM - Fold Recognition Server

• 3D-Jigsaw - Comparative Modeling Server

Free Software

• CNS - protein structure determination

• MAGE and PREKIN: - graphics programs

• RasMol: - graphics program

• MolMol - graphics program from the Wuthrich lab

• VMD - graphics program from the Schulten lab

• Cn3D - graphics program from NCBI

• SCWRL2.1 - A program for building sidechains given mainchain coordinates

• TINKER - Molecular modeling package

• MODELLER - Homology modeling package, free for academic users

• DSSP - Program to calculate the secondary structure assignment of a given protein structure

• Software from the Sanger Center

• THREADER 3 - Protein fold recognition

• DGEOM - Distance geometry

• GRAMM - Docking

• WHATIF - Molecular modeling

• DOCK - finding ligands for macromolecules

Almost Free Software

• CHARMM - molecular simulation package

• X-PLOR - protein structure determination

• AMBER - molecular simulation package

• GRASP - electrostatic potential maps

• DELPHI - Poisson-Boltzmann electrostatics

• UHBD - Poisson-Boltzmann and Brownian dynamics

Genomics, Proteomics

• Presage - Structural genomics

• Protein Structure Initiative - Structural genomics

• Whitehead Institute Genome Center

• NY Structural Genomics Research Consortium

Interesting Web sites

• Links to Web services
• Pedro's BioMolecular Research Tools- an excellent (if becoming somewhat outdated) collection of WWW resources for Biochemists
• Chemistry Links


• Skirball Institute, NYU
  
• Biology workbench, NCSA
  

Last Update: 3/28/00 by Themis Lazaridis
Email: themis@sci.ccny.cuny.edu