Tyka MD, Jung K, Baker D (2012) Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers . J Comput Chem 79 : 2483–2491 [ PMC free article ] [ PubMed ]Tyka M D,Jung K,Baker D.Efficient sampling of protein ...
PROTEIN analysisMOLECULAR dynamicsMONTE Carlo methodPROTEIN foldingTHERMODYNAMICSComputer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this ...
protein structure predictionconformational samplingtorsion angle predictionenergy functionProtein structure prediction is a long-standing prdoi:info:doi/10.1002/jcc.24285ZhouGriffithYaoqiGriffithYangGriffithYuedongGriffithJournal of Computational Chemistry: Organic, Inorganic, Physical, Biological...
Learn about a novel computational method called weighted ensemble, designed to explore rare protein conformational states crucial for drug discovery
One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes with either large system size or long timescales. To overcome this bottleneck, we present the REinforcement learning based Adaptive samPling (REAP) algorithm that aim...
Efficient exploration of protein conformational space remains challenging especially for large proteins when assembling discretized structural fragments extracted from a protein structure data database. We propose a fragment-free probabilistic graphical model, FUSION, for conformational sampling in continuous spac...
Protein folding has attracted considerable research effort in biochemistry in recent decades. In this work, we explore the potential of quantum computing to solve a simplified version of protein folding. More precisely, we numerically investigate the per
Protein structure prediction can be considered as a multimodal optimization problem for sampling the protein conformational space associated with an extremely complex energy landscape. To address this problem, a conformational space sampling method using multi-subpopulation differential evolution, MDE, is prop...
Protein folding has attracted considerable research effort in biochemistry in recent decades. In this work, we explore the potential of quantum computing to solve a simplified version of protein folding. More precisely, we numerically investigate the per
A number of studies comparing the predictions of protein conformational dynamics that arise from the use of different force fields in MD simulations have utilized ubiquitin and have often differed significantly in their predictions for that protein. Furthermore, ubiquitin has been the subject for the ...