title: FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.
abstract: Computational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm, implemented as a server, can modify an apo structure to yield mapping results that are similar to those of the respective bound structure. Thus, FTFlex is an extension of our FTMap server, which only considers rigid structures. FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library. In cases where the mapping results of the apo structure were in poor agreement with those of the bound structure, FTFlex was able to yield a modified apo structure, which lead to improved FTMap results. In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted.
  
  
  BACKGROUND
  FTFlex is freely available as a web-based server at http://ftflex.bu.edu/.
authors.affiliation: Department of Sciences, Wentworth Institute of Technology, Boston, MA 01746, USA.
authors.forename: Laurie E
authors.initials: LE
authors.lastname: Grove
authors.forename: David R
authors.initials: DR
authors.lastname: Hall
authors.forename: Dmitri
authors.initials: D
authors.lastname: Beglov
authors.forename: Sandor
authors.initials: S
authors.lastname: Vajda
authors.forename: Dima
authors.initials: D
authors.lastname: Kozakov
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D012997:Solvents / Q000737:chemistry
chemical_list: D008024:Ligands; D011506:Proteins; D012997:Solvents