SOFTWARE

FTMAP

COMPUTATIONAL SOLVENT MAPPING

FTMap is a  protein mapping server that identifies binding hot spotss, which are regions of protein surface that make major contributions to the ligand-binding free energy. FTMap samples billions of positions of small organic molecules used as probes, and it scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots in good agreement with experimental data. This server can help researchers determine druggability as well as provide information for drug discovery. The FTMap family of servers were featured on Nature Protocols in 2015.

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CLUSPRO

PROTEIN-PROTEIN

DOCKING

ClusPro is a fully automated rigid body protein-protein docking server, based on our FFT-based docking program PIPER. ClusPro is equipped with specialized modes for dimer classification (ClusPro-DC), and global docking of peptide motifs (PeptiDock), as well as advanced options for antibody-antigen docking, user-specified restraints, and SAXS profiles to assist in docking.

The ClusPro server has been consistently successful in the community-wide CAPRI (Critical Assessment of Prediction of Interactions) experiment. This work has been published in Nature Protocols.

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CLUSPRO TBM

TEMPLATE-BASED MODELING

ClusPro TBM offers template-based modeling for homomeric and heteromeric protein complexes. Given an input sequence and desired target stoichiometry, ClusPro TBM uses an HHpred-based template search through a local, comprehensive pdb100 database to identify all possible templates from the Protein Data Bank (PDB). Templates matching input requirements are modeled, then clustered to remove redundancy. A detailed description of the protocol can be found in our 2019 Proteins paper.

FTDyn

DYNAMIC ENSEMBLE MAPPING

FTDyn offers hot spot analysis on structural protein ensembles, using computational solvent mapping implemented in FTMap. FTDyn analyzes FTMap results by calculating the number of non-bonded and hydrogen bond interactions between all solvent probes and each residue using HBPlus. Results from FTDyn can be used to identify the structure most similar to a ligand-bound conformation. See our 2014 PLoS Computational Biology paper for more detail.

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FTSite

BINDING SITE

PREDICTION

As a member of the FTMap family, FTSite finds likely ligand-binding sites. The method is based on the observation that the binding site of a protein generally includes a strong main hot spot plus some other hot spots nearby. FTSite uses the hot spots detected by its parent FTMap to identify and rank binding sites. You can find more detailed descriptions of the server in our 2012 Bioinformatics paper.

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FTFlex

FLEXIBLE PROTEIN MAPPING

FTFlex belongs to the FTMap family of servers. FTFlex identifies binding hot spots of proteins and determines druggabilities, while exploring side-chain flexibility near the user-selected hot spots. The primary goal of FTFlex is to open pockets in the protein-protein interfaces that are potentially capable of binding small molecules. It uses a multi-stage mapping algorithm. More details can be found in our 2013 Bioinformatics paper.  

PeptiMap

PEPTIDE-BINDING

SITE DETECTION

PeptiMap is a server for accurate mapping of peptide binding sites on protein structures. Based on experimental evidence that peptide-binding sites also bind small organic molecules of various sizes and polarity, this protocol is built based on FTMap and further optimized to specifically account for peptide binding site characteristics. Our 2013 Proteins paper describes the algorithm in detail.

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KINASE ATLAS

KINASE DRUGGABILITY

ANALYSIS

The Kinase Atlas contains solvent mapping results for all kinases in the Protein Data Bank and provides information on whether a kinase can potentially be targeted by a type II, II, or IV inhibitor. Users can search through the Kinase Atlas database by PDB ID or by UniProt accession number. To read more about website, please see our 2019 J Med Chem paper.

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©2019 Vajda Lab