title: Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction.
abstract: BACKGROUND
  Protein-ligand binding sites are the active sites on protein surface that perform protein functions. Thus, the identification of those binding sites is often the first step to study protein functions and structure-based drug design. There are many computational algorithms and tools developed in recent decades, such as LIGSITE(cs/c), PASS, Q-SiteFinder, SURFNET, and so on. In our previous work, MetaPocket, we have proved that it is possible to combine the results of many methods together to improve the prediction result.
  
  
  RESULTS
  Here, we continue our previous work by adding four more methods Fpocket, GHECOM, ConCavity and POCASA to further improve the prediction success rate. The new method MetaPocket 2.0 and the individual approaches are all tested on two datasets of 48 unbound/bound and 210 bound structures as used before. The results show that the average success rate has been raised 5% at the top 1 prediction compared with previous work. Moreover, we construct a non-redundant dataset of drug-target complexes with known structure from DrugBank, DrugPort and PDB database and apply MetaPocket 2.0 to this dataset to predict drug binding sites. As a result, >74% drug binding sites on protein target are correctly identified at the top 3 prediction, and it is 12% better than the best individual approach.
  
  
  BACKGROUND
  The web service of MetaPocket 2.0 and all the test datasets are freely available at http://projects.biotec.tu-dresden.de/metapocket/ and http://sysbio.zju.edu.cn/metapocket.
authors.affiliation: Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, 310029 Hangzhou, China.
authors.forename: Zengming
authors.initials: Z
authors.lastname: Zhang
authors.forename: Yu
authors.initials: Y
authors.lastname: Li
authors.forename: Biaoyang
authors.initials: B
authors.lastname: Lin
authors.forename: Michael
authors.initials: M
authors.lastname: Schroeder
authors.forename: Bingding
authors.initials: B
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D015195:Drug Design; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins