TY - JOUR ID - 496 TI - Comparing the performance of a knowledge-based potential and a knowledge-based force functions in the scoring of protein-protein complexes JO - Cellular and Molecular Research (Iranian Journal of Biology) JA - CMR LA - en SN - 2383-2738 AU - Jafari, Rahim AU - Mirzaei, Mehdi AU - Erfani Moghaddam, Majid AU - Sadeghi, Mehdi AD - PhD student of Nanobiotechnology, Tarbiat modares University AD - Scientific board, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences AD - Scientific board, Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University AD - National Institute of Genetic Engineering and Biotechnology Y1 - 2015 PY - 2015 VL - 27 IS - 4 SP - 495 EP - 505 KW - knowledge-based potential KW - force KW - scoring function KW - protein-protein docking DO - 2743 N2 - The knowledge-based force function is a new type of the scoring functions that has been used in the field of protein fold recognition with a noticeable success. In this study we compared the performance of a knowledge-based potential function and its corresponding force function in discrimination of the correct protein-protein complexes from the incorrect ones. The total force imposed by one component (receptor/ligand) upon another was used as a measure of complex stability. This force is expected to be the lowest in the native structure. To test the performance of each method, two decoy sets were used; one generated by soft body docking and the other by rigid body docking algorithms. The results of this comparison show that, for both decoy sets, the success rates in native and near native selections of the energy model are higher than that of the force model. It seems, the dependence of amount of the force on shape of the interface region introduces errors in the later model and therefore makes it inappropriate for the scoring of docked complexes. UR - https://cell.ijbio.ir/article_496.html L1 - https://cell.ijbio.ir/article_496_4121d8516e02451be153c17431d20a47.pdf ER -