Lattice protein folding with two and four-body statistical potentials.

@article{citeulike:458037, abstract = {The cooperative folding of proteins implies a description by multibody potentials. Such multibody potentials can be generalized from common two-body statistical potentials through a relation to probability distributions of residue clusters via the Boltzmann condition. In this exploratory study, we compare a four-body statistical potential, defined by the Delaunay tessellation of protein structures, to the Miyazawa-Jernigan (MJ) potential for protein structure prediction, using a lattice chain growth algorithm. We use the four-body potential as a discriminatory function for conformational ensembles generated with the MJ potential and examine performance on a set of 22 proteins of 30-76 residues in length. We find that the four-body potential yields comparable results to the two-body MJ potential, namely, an average coordinate root-mean-square deviation (cRMSD) value of 8 A for the lowest energy configurations of all-alpha proteins, and somewhat poorer cRMSD values for other protein classes. For both two and four-body potentials, superpositions of some predicted and native structures show a rough overall agreement. Formulating the four-body potential using larger data sets and direct, but costly, generation of conformational ensembles with multibody potentials may offer further improvements. Proteins 2001;43:161-174.}, address = {Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, New York, NY 10012, USA.}, author = {Gan, H. H. and Tropsha, A. and Schlick, T. }, citeulike-article-id = {458037}, issn = {0887-3585}, journal = {Proteins}, keywords = {potential, protein, statistical}, month = {May}, number = {2}, pages = {161--174}, posted-at = {2006-01-06 15:24:56}, priority = {2}, title = {Lattice protein folding with two and four-body statistical potentials.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/11276086}, volume = {43}, year = {2001} }

TY - JOUR ID - citeulike:458037 L3 - citeulike-article-id:458037 TI - Lattice protein folding with two and four-body statistical potentials. JF - Proteins VL - 43 IS - 2 SP - 161 EP - 174 AD - Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, New York, NY 10012, USA. SN - 0887-3585 N2 - The cooperative folding of proteins implies a description by multibody potentials. Such multibody potentials can be generalized from common two-body statistical potentials through a relation to probability distributions of residue clusters via the Boltzmann condition. In this exploratory study, we compare a four-body statistical potential, defined by the Delaunay tessellation of protein structures, to the Miyazawa-Jernigan (MJ) potential for protein structure prediction, using a lattice chain growth algorithm. We use the four-body potential as a discriminatory function for conformational ensembles generated with the MJ potential and examine performance on a set of 22 proteins of 30-76 residues in length. We find that the four-body potential yields comparable results to the two-body MJ potential, namely, an average coordinate root-mean-square deviation (cRMSD) value of 8 A for the lowest energy configurations of all-alpha proteins, and somewhat poorer cRMSD values for other protein classes. For both two and four-body potentials, superpositions of some predicted and native structures show a rough overall agreement. Formulating the four-body potential using larger data sets and direct, but costly, generation of conformational ensembles with multibody potentials may offer further improvements. Proteins 2001;43:161-174. KW - potential KW - protein KW - statistical AU - Gan, HH AU - Tropsha, A AU - Schlick, T PY - 2001/05/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/11276086 ER -