Software and Services

Online Services

  • PSiFR: A web portal that provides access to TASSER, TASSER-Lite and MetaTASSER and DBD-Hunter, and the enzyme function inference engine EFICAz2.

Protein Structure Prediction

  • chunk-TASSER: A protein structure prediction method that combines threading templates from SP3 and ab initio folded chunk structures (three consecutive segments of regular secondary structures).
  • MetaTASSER: A protein structure prediction server that uses three state-of-the-art threading methods PROSPECTOR_3, SP3 and SPARKS to identify templates that are selected by 3D-Jury. For targets with no reliable templates, chunk models from chunk-TASSER are also included. SPICKER clustering is used to select the final models from the TASSER trajectory. Detailed atomic models are then built using PULCHRA.
  • pro-sp3-TASSER: Uses a single threading method with multiple scoring to identify templates. Short TASSER runs generate full length models that are selected by TASSER-QA and FTCOM ranking procedures. pro-sp3-TASSER performs better than MetaTASSER for medium/hard targets but is computationally more expensive.

Protein Structure Refinement

  • BSR: Binding Site Refinement employs a new template-based method for the local refinement of ligand-binding regions in protein models using closely as well as distantly related templates identified by threading.

Protein Structure Alignment

  • Fr-TM-align: Structural alignment program for monomeric proteins that uses the TM-score as the structure comparison metric.
  • iAlign: Structural alignment algorithm for protein-protein interfaces that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.

DNA-binding Prediction

  • DBD-Threader: A server that identifies DNA-binding domains from a protein's sequence.
  • DBD-Hunter: A server that identifies a DNA-binding domain from a protein’s structure.
  • DP-dock: A server that predicts the structure of a DNA/protein complex given the structure of a DNA-binding protein.

Protein Function Prediction

  • FINDSITE: A threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
  • FINDSITE-metal: A simple extension of FINDSITE that predicts metal-binding sites, residues and binding metal preferences from evolutionarily related templates detected by threading. Furthermore, it employs machine learning to significantly improve the prediction accuracy particularly against modeled protein structures.
  • EFICAz2.5: An accurate sequence based approach to enzyme function inference.

Ligand Docking/Screening

  • FINDSITELHM: A homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds for similarity-based ligand binding pose prediction.
  • Q-DockLHM: A low-resolution ligand docking/refinement approach applicable to the modeled structures of target receptors. It uses pocket-specific statistical potentials and harmonic restraints imposed on the binding poses of the common molecule substructures extracted from evolutionarily related proteins.


Software (available for download)


  • EFICAz2.5: An accurate sequence based approach to enzyme function inference.
  • FINDSITE: A threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins.
  • FINDSITELHM: A homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction.
  • Fr-TM-align: A program for protein structural alignment that uses the TM-score as the structural comparison metric. This is an improved version of Tm-align.
  • iAlign: Structural alignment algorithm for protein-protein interfaces that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.
  • PULCHRA: A program for all-atom reconstruction from the backbone C-alpha atoms.
  • TASSER-Lite: A comparative protein structure modeling tool.

Databases




Simulations