ParaDock: a flexible non-specific DNA--rigid protein docking algorithm
نویسندگان
چکیده
منابع مشابه
ParaDock: a flexible non-specific DNA—rigid protein docking algorithm
Accurate prediction of protein-DNA complexes could provide an important stepping stone towards a thorough comprehension of vital intracellular processes. Few attempts were made to tackle this issue, focusing on binding patch prediction, protein function classification and distance constraints-based docking. We introduce ParaDock: a novel ab initio protein-DNA docking algorithm. ParaDock combine...
متن کاملA Combinatorial Shape Matching Algorithm for Rigid Protein Docking
The protein docking problem is to predict the structure of protein-protein complexes from the structures of individual proteins. It is believed that shape complementarity plays a dominant role in protein docking. Recently, it has been shown empirically by Bespamaytnikh et al [4] that the shape complementarity (measured by a score function) is sufficient for the bound protein docking problem, in...
متن کاملFlexible Protein-Protein Docking
Biological processes almost always involve protein-protein interactions. Understanding the function of protein-protein interactions requires knowledge of the structure of the corresponding protein-protein complexes. The experimental structure determination by Xray crystallography requires purification of large amounts of proteins. In addition, it is necessary to crystallize the proteins in the ...
متن کاملFlexible protein-protein docking based on Best-First search algorithm
We developed a new high resolution protein-protein docking method based on Best-First search algorithm that loosely imitates protein-protein associations. The method operates in two stages: first, we perform a rigid search on the unbound proteins. Second, we search alternately on rigid and flexible degrees of freedom starting from multiple configurations from the rigid search. Both stages use h...
متن کاملFlexible Ligand-Protein Docking
The parameters ∆H R, ∆S ◦ R and ∆Cp can all be calculated from knowledge of various changes in accessible surface area (ASA), which is defined as the surface traced out by a sphere, with radius equal to that of a solvent molecule, when rolled over the surface of the molecule of interest. This can also be formulated in configuration space as the Minkowski sum of the protein and the sphere, namel...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2011
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkr620