Bioinformatic Tools & Databases

See also Computational-Biophysical Tools page.

(Note: some of the URLs have changed over time, so if you are redirected to a blank page just Google the name of the software/database/web-server to find the new URL)

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1. Protein & Enzyme Databases

I. Classification & General Info

• Proteopedia – 3D encyclopedia of proteins and other molecules
• SCOP– Structural Classification Of Proteins
• CATH (another classification database)
• GeneCards (database of human genes)

II. Sequence

• SwissProt – a comprehensive protein sequences database
• Pfam – sequence-based identification of domains
• PredictProtein – sequence-based prediction of protein features, e.g. secondary structures

III. Structure

• PDB – Protein Data Bank
• PDBSum (concise info on each PDB entry)

IV. Enzymes

• BRENDA (a comprehensive enzyme information system)
• Enzyme nomenclature (E.C. system)
• Enzyme Classification Database
• MACiE (database of enzymatic reactions)
• IntEnz (integrated relational enzyme datablase)
• Catalytic Site Atlas (enzymes catalytic sites)
• EzCatDB (enzymes catalytic sites)
• EC-PDB (enzymes with known 3D structure)
• Thermodynamics of enzyme-catalyzed reactions
• PRECISE (predicted and consensus interaction sites in enzymes)
• More enzyme-related databases

V. Membrane Proteins

• Membrane Proteins of Known Structure

VI. Disease-related

• OMIM (proteins involved in genetic diseases)

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2. Small Molecules Databases

• ChemFinder
  
• Small molecules database
• PubChem
• DrugBank

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3. Bioinformatic Tools

I. Sequence Analysis

• Blast (finding protein sequence homologs)
• ClustalW (multiple sequence alignment)
  
• ConSurf (locating evolutionary conserved regions in proteins) [see figure at bottom of page]
• Phylip (proteins evolutionary trees)

II. Secondary Structure Prediction

• Jpred
• META Server

III. 3D Structure Prediction (fully-automated servers)

• AlphaFold2 (DeepMind):
  • DM’s server
  • DM’s AlphaFold Multimer (for small complexes, preferably dimers)
  • DM’s database (pre-calculated structures)
  • ColabFold (fast)
  • UniFold (fast, predicts also multimers)
  • MoLPC (for large complexes; uses AlphaFold+Monte Carlo simulations)
• RoseTTAFold (David Baker)
• OmegaFold (from primariy sequence, very fast)
• RGN2 (from primary sequence)
• ModWeb (Modeller for homology modeling, Andrej Sali)
• ROBETTA (David Baker)
• I-TASSER (Yang Zhang)
• HHPred (hidden Markov model method for finding homology modeling templates)

IV. Domain Structural Identification

• META-DP (Daniel Fischer’s Lab)

(more info on these and other structure prediction servers can be found in this paper by Daniel Fischer)

V. Protein Dynamics

• ConTemplate server: prediction of protein conformations

VI. Protein Function Prediction

• 3D-Fun: Predicting protein function from structure (G. Vriend’s lab)

• SNAP: Predicting the effect of mutations on protein function (B. Rost lab)

• PatchFinder: Identification of functional regions in proteins (N. Ben-Tal lab)

• iDBPs: Identification of DNA-binding proteins (N. Ben-Tal Lab)

• DNABindProt: Determination of potential DNA binding sites (T. Haliloglu Lab).

VII. Prediction of mutation outcome

• Deleterious/non-deleterious prediction:
  • AlphaMissense (database by DeepMind)
  • PredictSNP (Damborski lab)
  • PolyPhen2
• Effect on protein stability
  • Duet (Blundell)
  • INPS-MD
  • DynaMut

The evolutionary conservation of caveolin-1 (PDB ID 7SC0), as calculated by the ConSurf webserver. The conservation is shown as a color code (see scale at the bottom of the image)

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