title: Predicting protein complex geometries with linear scoring functions.
abstract: Protein-Protein interactions play an important role in many cellular processes. However experimental determination of the protein complex structure is quite difficult and time consuming. Hence, there is need for fast and accurate in silico protein docking methods. These methods generally consist of two stages: (i) a sampling algorithm that generates a large number of candidate complex geometries (decoys), and (ii) a scoring function that ranks these decoys such that nearnative decoys are higher ranked than other decoys. We have recently developed a neural network based scoring function that performed better than other state-of-the-art scoring functions on a benchmark of 65 protein complexes. Here, we use similar ideas to develop a method that is based on linear scoring functions. We compare the linear scoring function of the present study with other knowledge-based scoring functions such as ZDOCK 3.0, ZRANK and the previously developed neural network. Despite its simplicity the linear scoring function performs as good as the compared state-of-the-art methods and predictions are simple and rapid to compute.
authors.affiliation: Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36A, 14195 Berlin, Germany. odemir@chemie.fu-berlin.de.
authors.forename: Ozgur
authors.initials: O
authors.lastname: Demir-Kavuk
authors.forename: Florian
authors.initials: F
authors.lastname: Krull
authors.forename: Myong-Ho
authors.initials: MH
authors.lastname: Chae
authors.forename: Ernst-Walter
authors.initials: EW
authors.lastname: Knapp
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D062105:Molecular Docking Simulation; D016571:Neural Networks, Computer; D011381:Programming Languages; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D011506:Proteins