Antibody side chain conformations are position-dependent
نویسندگان
چکیده
منابع مشابه
Modeling Antibody Side Chain Conformations Using Heuristic Database Search
We have developed a knowledge-based system which models the side chain conformations of residues in the variable domains of antibody Fv fragments. The system is written in Prolog and uses an object-oriented database of aligned antibody structures in conjunction with a side chain rotamer library. The antibody database provides 3-dimensional clusters of side chain conformations which can be copie...
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Antibody modelling by side chain placement on an homologous backbone conformation is a combinatorially hard problem. This can be made tractable by using a knowledge-based approach in which a heuristic cost function is used to perform a structural search on a database of known structures in order to nd re-usable clusters of side chains. The procedure described yields a plausible structure which ...
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Determination of side-chain conformations is an important step in protein structure prediction and protein design. Many such methods have been presented, although only a small number are in widespread use. SCWRL is one such method, and the SCWRL3 program (2003) has remained popular because of its speed, accuracy, and ease-of-use for the purpose of homology modeling. However, higher accuracy at ...
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We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modelin...
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Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the r...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics
سال: 2018
ISSN: 0887-3585
DOI: 10.1002/prot.25453