The penultimate rotamer library
نویسندگان
چکیده
منابع مشابه
The penultimate rotamer library.
All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar termi...
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An increasingly used parameter in structural biology is the measurement of distances between spin labels bound to a protein. One limitation to these measurements is the unknown position of the spin label relative to the protein backbone. To overcome this drawback, we introduce a rotamer library of the methanethiosulfonate spin label (MTSSL) into the protein modeling program Rosetta. Spin label ...
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Existing flexible docking approaches model the ligand and receptor flexibility either separately or in a loosely coupled manner, which captures the conformational changes inefficiently. Here, we propose a flexible docking approach, MedusaDock, which models both ligand and receptor flexibility simultaneously with sets of discrete rotamers. We developed an algorithm to build the ligand rotamer li...
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Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side-chains with satisfactory justification for their given conformation, we added residue-...
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. The work reported in this paper present the use of Genetic Algorithms (GA) with distinct field forces and rotamer library dependent of backbone to predict the tertiary structure of peptides. We discuss an improved version in which the backbone and side chain were relaxed and a rotamer library dependent of the backbone was used library give the four most probably values of the angles χi for th...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Genetics
سال: 2000
ISSN: 0887-3585,1097-0134
DOI: 10.1002/1097-0134(20000815)40:3<389::aid-prot50>3.3.co;2-u