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Protein-protein docking procedures typically perform the global scan of the proteins relative positions, followed by the local refinement of the putative matches. Because of the size of the search space, the global scan is usually implemented as rigid-body search, using computationally inexpensive intermolecular energy approximations. An adequate refinement has to take into account structural flexibility. Since the refinement performs conformational search of the interacting proteins, it is extremely computationally challenging, given the enormous amount of the internal degrees of freedom. Different approaches limit the search space by restricting the search to the side chains, rotameric states, coarse-grained structure representation, principal normal modes, and so on. Still, even with the approximations, the refinement presents an extreme computational challenge due to the very large number of the remaining degrees of freedom. Given the complexity of the search space, the advantage of the exhaustive search is obvious. The obstacle to such search is computational feasibility. However, the growing computational power of modern computers, especially due to the increasing utilization of Graphics Processing Unit (GPU) with large amount of specialized computing cores, extends the ranges of applicability of the brute-force search methods. This proof-of-concept study demonstrates computational feasibility of an exhaustive search of side-chain conformations in protein pocking. The procedure, implemented on the GPU architecture, was used to generate the optimal conformations in a large representative set of protein-protein complexes. © 2018 Wiley Periodicals, Inc.
This article was published in the following journal.
Name: Journal of computational chemistry
Phytoecdysteroids exert their non-hormonal anabolic and adaptogenic effects in mammals, including humans, through a partially revealed mechanism of action involving the activation of protein kinase B ...
α- N-(Fmoc)Amino-γ-lactam dipeptides with a variety of β-substituents were synthesized stereoselectively with minimal β-elimination by routes employing, respectively, Mitsunobu chemistry and cycli...
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Precise construction of a three-dimensional molecular structure is key for functional macromolecules, such as enzymes or proteins. We previously proposed a new concept, "expanded poly(alpha-amino acid...
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Computational simulation will be performed to represent motion of knees with a dislocating kneecap. Common surgical treatment methods will be simulated and anatomical parameters commonly a...
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The purpose of this study is to compare a normal-protein diet containing branched-chain amino acids to a low-protein diet in patients with non-terminal cirrhosis (MELD < 25) who have devel...
A group of antibiotics that contain 6-aminopenicillanic acid with a side chain attached to the 6-amino group. The penicillin nucleus is the chief structural requirement for biological activity. The side-chain structure determines many of the antibacterial and pharmacological characteristics. (Goodman and Gilman's The Pharmacological Basis of Therapeutics, 8th ed, p1065)
A heterodimeric protein that is a cell surface antigen associated with lymphocyte activation. The initial characterization of this protein revealed one identifiable heavy chain (FUSION REGULATORY PROTEIN 1, HEAVY CHAIN) and an indeterminate smaller light chain. It is now known that a variety of light chain subunits (FUSION REGULATORY PROTEIN 1, LIGHT CHAINS) can dimerize with the heavy chain. Depending upon its light chain composition a diverse array of functions can be found for this protein. Functions include: type L amino acid transport, type y+L amino acid transport and regulation of cellular fusion.
A mitochondrial cytochrome P450 enzyme that catalyzes the side-chain cleavage of C27 cholesterol to C21 pregnenolone in the presence of molecular oxygen and NADPH-FERRIHEMOPROTEIN REDUCTASE. This enzyme, encoded by CYP11A1 gene, catalyzes the breakage between C20 and C22 which is the initial and rate-limiting step in the biosynthesis of various gonadal and adrenal steroid hormones.
A heterodimeric protein that is a cell surface antigen associated with lymphocyte activation. The initial characterization of this protein revealed one identifiable heavy chain (ANTIGENS, CD98 HEAVY CHAIN) and an indeterminate smaller light chain. It is now known that a variety of light chain subunits (ANTIGENS, CD98 LIGHT CHAINS) can dimerize with the heavy chain. Depending upon its light chain composition a diverse array of functions can be found for this protein. Functions include: type L amino acid transport, type y+L amino acid transport and regulation of cellular fusion.
Polyunsaturated side-chain quinone derivative which is an important link in the electron transport chain of green plants during the photosynthetic conversion of light energy by photophosphorylation into the potential energy of chemical bonds.
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