Sampling Realistic Protein Conformations Using Local Structural Bias

@article{citeulike:877204, abstract = {The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design.}, author = {Hamelryck, Thomas and Kent, John T. and Krogh, Anders }, citeulike-article-id = {877204}, doi = {http://dx.doi.org/10.1371/journal.pcbi.0020131}, journal = {PLoS Computational Biology}, keywords = {biophysics, clustering, computational\_biology, dynamics, structure}, month = {September}, number = {9}, pages = {e131+}, posted-at = {2006-09-29 08:57:03}, priority = {2}, title = {Sampling Realistic Protein Conformations Using Local Structural Bias}, url = {http://dx.doi.org/10.1371/journal.pcbi.0020131}, volume = {2}, year = {2006} }

TY - JOUR ID - citeulike:877204 L3 - citeulike-article-id:877204 TI - Sampling Realistic Protein Conformations Using Local Structural Bias JF - PLoS Computational Biology VL - 2 IS - 9 SP - e131 N2 - The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design. KW - biophysics KW - clustering KW - computational_biology KW - dynamics KW - structure AU - Hamelryck, Thomas AU - Kent, John AU - Krogh, Anders PY - 2006/09/01/ UR - http://dx.doi.org/10.1371/journal.pcbi.0020131 ER -