Software and Services

Online Services

    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.
    • TASSER-VMT: A protein structure modeling method that uses Variable number Multiple Templates to generate an ensemble of models. Target-template alignments were generated using SP3 alternative alignment and HHpred methods. Three model quality assessment methods TASSERQA, FTCOM & GOAP are used to select models for further TASSER refinement.

    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-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.

    Ligand Docking/Screening

    • FINDSITECOMB: Is a tool for large scale virtual ligand screening. It offers the advantage that comparable results are obtained when predicted or experimental structures are used. The user can either provide a protein structure in PDB format or a protein sequence whose structure will first be predicted prior its use in virtual ligand screening.

    Personalized Medicine

    • ENTPRISE: An algorithm for predicting human disease-associated amino acid mutations from sequence entropy and predicted protein structures.
    • DR.PRODIS: A comprehensive prediction of drug-protein interactions, side effects, toxicity and disease associations for the human proteome.

    Software (available for download)

    • APoc: Is an efficient tool for large-scale structural comparison of protein pockets for interacting with small-molecule ligands.
    • Cavitator: Is a program for detecting "pocket" or "cavity", i.e., potential small-molecule binding sites, in a protein structure.
    • EFICAz2.5: An accurate sequence based approach to enzyme function inference.
    • 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.
    • GOAP: A generalized orientation-dependent, all-atom statistical potential for protein structure prediction.
    • 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.
    • IS-score: Is a tool for automatic assessing the quality of protein-protein docking models.
    • LIGSIFT: A new computational method for the structural alignment of small molecules.
    • PULCHRA: A program for all-atom reconstruction from the backbone C-alpha atoms.