The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

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Abstract

FTMap is a computational mapping server that identifies binding hot spots of macromolecules—i.e., regions of the surface with major contributions to the ligand-binding free energy. To use FTMap, users submit a protein, DNA or RNA structure in PDB (Protein Data Bank) format. 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. FTMap serves as the basis for other servers, namely FTSite, which is used to predict ligand-binding sites, FTFlex, which is used to account for side chain flexibility, FTMap/param, used to parameterize additional probes and FTDyn, for mapping ensembles of protein structures. Applications include determining the druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures and providing input for fragment-based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and it is much faster than the more-recent approaches to protein mapping based on mixed molecular dynamics. By using 16 probe molecules, the FTMap server finds the hot spots of an average-size protein in <1 h. As FTFlex performs mapping for all low-energy conformers of side chains in the binding site, its completion time is proportionately longer.

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Figure 1: Principles and tools of the FTMap algorithm.
Figure 2: Flowchart of the FTMap algorithm.
Figure 3: Flowchart of the FTFlex algorithm.
Figure 4: Screenshot of FTMap results for PDB ID 2ren (apo structure of renin).
Figure 5: Viewing FTMap results for PDB ID 2ren (apo structure of renin) using PyMOL.
Figure 6: Screen capture of FTSite results for human lymphocyte kinase (Lck, PDB ID 3lck).
Figure 7: Transition from stage 1 to stage 2 in FTFlex: selection of consensus clusters around which low-energy side chain conformers will be explored in repeated mapping calculations.
Figure 8: Screenshot of the PyMOL session from the application of FTMap/param to the unbound structure of thrombin (PDB ID 1hxf) with the user-defined probe molecule 1-(3-chlorophenyl)methanamine, a thrombin inhibitor.
Figure 9: Screenshots of the result page when applying FTDyn to map an ensemble of 24 structures of the MDM2 protein (PDB ID 1z1m), determined by NMR.
Figure 10: Mapping of the 24 MDM2 structures obtained by NMR using FTDyn.
Figure 11: Comparison of FTMap results with experimental data.
Figure 12: Consensus sites identified using FTMap for thrombin (PDB ID 1ths) are shown in line representation, overlapping with fragments and a high-affinity ligand shown as sticks.
Figure 13: Flexible mapping of the apo structure of CDK2 (PDB ID 1pw2) using FTFlex.

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Protein Data Bank

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Acknowledgements

This investigation was supported by grants GM064700 from the National Institute of General Medical Sciences.

Author information

D.K., D.R.H., T.B., B.X. and S.E.M. developed the servers; D.K., L.E.G., D.R.H., T.B., D.B., L.L. and B.X. performed experiments; L.E.G., D.R.H. and S.V. prepared the manuscript with editing by T.B., S.V. and L.E.G.

Correspondence to Dima Kozakov or Sandor Vajda.

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Competing interests

D.R.H. is a full-time employee of Acpharis Inc., and the company licenses software related to protein mapping. D.K., D.B. and S.V. own stock in Acpharis. However, all programs and servers described here are free for research use.

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Kozakov, D., Grove, L., Hall, D. et al. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nat Protoc 10, 733–755 (2015) doi:10.1038/nprot.2015.043

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