Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 2 of 2
Full-Text Articles in Entire DC Network
Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón
Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón
Computer Science Faculty Publications
Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop …
Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li
Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li
Computer Science Faculty Publications
Background: Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional characteristics of many proteins.
Methods: In this work, we introduce an approach of enhancing disulfide bonding prediction accuracy by taking advantage of context-based features. We firstly derive the first-order and second-order mean-force potentials according to the amino acid environment around the cysteine residues from large number of cysteine samples. The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as …