title: Memdock: an α-helical membrane protein docking algorithm.
abstract: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein-protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment.
  
  
  
  We present a novel algorithm, Memdock, for docking α-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to a standard protein-protein docking algorithm.
  
  
  
  http://bioinfo3d.cs.tau.ac.il/Memdock/
  
  
  
  namih@tau.ac.il or wolfson@tau.ac.il
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Naama
authors.initials: N
authors.lastname: Hurwitz
authors.affiliation: Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
authors.forename: Dina
authors.initials: D
authors.lastname: Schneidman-Duhovny
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
authors.forename: Haim J
authors.initials: HJ
authors.lastname: Wolfson
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D008565:Membrane Proteins; D008958:Models, Molecular
chemical_list: D008565:Membrane Proteins