Use of pair potentials across protein interfaces in screening predicted docked complexes
نویسندگان
چکیده
منابع مشابه
A novel method for scoring of docked protein complexes using predicted protein-protein binding sites.
Docking algorithms produce many possible structures of a protein-protein complex. In most cases some of them resemble the correct structure within an r.m.s.d. of <3 A. A major challenge in the field of docking is to extract the correct structure out of this pool, the so-called 'scoring'. Here, we introduce a new scoring function, which discriminates between the many wrong and few true conformat...
متن کاملScoring Docked Protein Complexes with Hydrogen Bonds
Finding the structure of proteins and protein-protein complexes is an important problem in the field of computational biology. Determining protein structures can be done successfully with various experimental methods like x-ray crystallography, but determining protein-protein structures experimentally is more difficult. Instead, these structures are frequently predicted computationally. One app...
متن کاملpredictions of protein-protein interfaces within membrane protein complexes
background: prediction of interaction sites within the membrane protein complexes using the sequence data is of a great importance, because it would find applications in modification of molecules transport through membrane, signaling pathways and drug targets of many diseases. nevertheless, it has gained little attention from the protein structural bioinformatics community. methods: in this stu...
متن کاملA machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison
Reliable identification of near-native poses of docked protein-protein complexes is still an unsolved problem. The intrinsic heterogeneity of protein-protein interactions is challenging for traditional biophysical or knowledge based potentials and the identification of many false positive binding sites is not unusual. Often, ranking protocols are based on initial clustering of docked poses foll...
متن کاملPredictions of Protein-Protein Interfaces within Membrane Protein Complexes
BACKGROUND Prediction of interaction sites within the membrane protein complexes using the sequence data is of a great importance, because it would find applications in modification of molecules transport through membrane, signaling pathways and drug targets of many diseases. Nevertheless, it has gained little attention from the protein structural bioinformatics community. METHODS In this stu...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Genetics
سال: 1999
ISSN: 0887-3585,1097-0134
DOI: 10.1002/(sici)1097-0134(19990515)35:3<364::aid-prot11>3.0.co;2-4