title: The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.
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.
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors: Dima
authors: D
authors: Kozakov
authors: Department of Sciences, Wentworth Institute of Technology, Boston, Massachusetts, USA.
authors: Laurie E
authors: LE
authors: Grove
authors: Acpharis Inc., Holliston, Massachusetts, USA.
authors: David R
authors: DR
authors: Hall
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors: Tanggis
authors: T
authors: Bohnuud
authors: Program in Bioinformatics, Boston University, Boston, Massachusetts, USA.
authors: Scott E
authors: SE
authors: Mottarella
authors: Program in Bioinformatics, Boston University, Boston, Massachusetts, USA.
authors: Lingqi
authors: L
authors: Luo
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors: Bing
authors: B
authors: Xia
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors: Dmitri
authors: D
authors: Beglov
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.
authors: Sandor
authors: S
authors: Vajda
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008024:Ligands; D015335:Molecular Probes; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D008024:Ligands; D015335:Molecular Probes; D011506:Proteins