Track topics on Twitter Track topics that are important to you
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
We determined an empirical correlation that relates the Amide I vibrational band frequencies of the glutamine (Q) side chain to the strength of hydrogen bonding, van der Waals, and Lewis acid-base int...
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...
Pd(ii) and Pt(ii) compounds bearing N,N-pyridylbenzimidazole derivatives with an alkylated sulfonate or phosphonium side chain are able to bind the model protein lysozyme both covalently and non-coval...
Amino acid selective isotope labeling is an important nuclear magnetic resonance technique, especially for larger proteins, providing strong bases for the unambiguous resonance assignments and informa...
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...
With aging, there is a decrease in muscle mass and function especially in the energy storehouses of cells called mitochondria. Amino acids, the building blocks of protein, and insulin hav...
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...
In this study, we will explore the feasibility of doing a randomized controlled trial in our Intensive care department, King Abdulaziz Medical City, Riyadh which will test a two-step appro...
Neuropathic facial pain is one form of chronic facial pain lacking effective pharmacotherapy. Interest in the role of complementary and alternative medicine is growing and diet is at the...
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.
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...