Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction

@article{citeulike:341254, abstract = {A backbone-dependent rotamer library for amino acid side-chains is developed and used for constructing protein side-chain conformations from the main-chain co-ordinates. The rotamer library is obtained from 132 protein chains in the Brookhaven Protein Database. A grid of 20[deg] by 20[deg] blocks for the main-chain angles [phi],[psi] is used in the rotamer library. Significant correlations are found between side-chain dihedral angle probabilities and backbone [phi],[psi] values. These probabilities are used to place the side-chain on the known backbone in the test application for six proteins for which high-resolution crystal structures are available. A minimization scheme is used to reorient side-chains that conflict with the backbone or other side-chains after the initial placement. The initial placement yields 59\% of both [chi]1 and [chi]2 values in the correct position (to within 40[deg]) for thermolysin to 81\% for crambin. After refinement the values range from 61\% (lysozyme) to 89\% (crambin). It is evident from the results that a single protein does not adequately test a prediction scheme.The computation time required by the method scales linearly with the number of side-chains. An initial prediction from the library takes only a few seconds of computer time, while the iterative refinement takes on the order of hours. The method is automated and can easily be applied to aid experimental side-chain determinations and homology modeling. The high degree of correlation between backbone and side-chain conformations may introduce a simplification in the protein folding process by reducing the available conformational space.}, author = {Dunbrack, Jr and Karplus, Martin }, citeulike-article-id = {341254}, doi = {http://dx.doi.org/10.1006/jmbi.1993.1170}, journal = {Journal of Molecular Biology}, keywords = {rotamers}, month = {March}, number = {2}, pages = {543--574}, posted-at = {2008-06-01 17:04:13}, priority = {2}, title = {Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction}, url = {http://dx.doi.org/10.1006/jmbi.1993.1170}, volume = {230}, year = {1993} }

TY - JOUR ID - citeulike:341254 L3 - citeulike-article-id:341254 TI - Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction JF - Journal of Molecular Biology VL - 230 IS - 2 SP - 543 EP - 574 N2 - A backbone-dependent rotamer library for amino acid side-chains is developed and used for constructing protein side-chain conformations from the main-chain co-ordinates. The rotamer library is obtained from 132 protein chains in the Brookhaven Protein Database. A grid of 20[deg] by 20[deg] blocks for the main-chain angles [phi],[psi] is used in the rotamer library. Significant correlations are found between side-chain dihedral angle probabilities and backbone [phi],[psi] values. These probabilities are used to place the side-chain on the known backbone in the test application for six proteins for which high-resolution crystal structures are available. A minimization scheme is used to reorient side-chains that conflict with the backbone or other side-chains after the initial placement. The initial placement yields 59% of both [chi]1 and [chi]2 values in the correct position (to within 40[deg]) for thermolysin to 81% for crambin. After refinement the values range from 61% (lysozyme) to 89% (crambin). It is evident from the results that a single protein does not adequately test a prediction scheme.The computation time required by the method scales linearly with the number of side-chains. An initial prediction from the library takes only a few seconds of computer time, while the iterative refinement takes on the order of hours. The method is automated and can easily be applied to aid experimental side-chain determinations and homology modeling. The high degree of correlation between backbone and side-chain conformations may introduce a simplification in the protein folding process by reducing the available conformational space. KW - rotamers AU - Dunbrack, Jr AU - Karplus, Martin PY - 1993/03/20/ UR - http://dx.doi.org/10.1006/jmbi.1993.1170 ER -