OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations
We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of
coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics …
coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics …
A novel algorithm based on a modified PSO to predict 3D structure for proteins in HP model using Transfer Learning
M Rezaei, M Kheyrandish, M Mosleh - Expert Systems with Applications, 2024 - Elsevier
Most intracellular activities of living organisms are performed by proteins that have unique
and complex 3-Dimensional (3D) structures, playing very important roles in their operations …
and complex 3-Dimensional (3D) structures, playing very important roles in their operations …
AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes
The accurate and reliable prediction of the 3D structures of proteins and their assemblies
remains difficult even though the number of solved structures soars and prediction …
remains difficult even though the number of solved structures soars and prediction …
Molecular dissection studies of TAC1, a transcription activator of Candida drug resistance genes of the human pathogenic fungus Candida albicans
The up-regulation of ABC transporters Cdr1p and Cdr2p that efflux antifungal azole drugs
are a leading cause of Multi-Drug Resistance (MDR) in the white fungus Candida albicans …
are a leading cause of Multi-Drug Resistance (MDR) in the white fungus Candida albicans …
Structural and dynamical order of a disordered protein: molecular insights into conformational switching of PAGE4 at the systems level
Folded proteins show a high degree of structural order and undergo (fairly constrained)
collective motions related to their functions. On the other hand, intrinsically disordered …
collective motions related to their functions. On the other hand, intrinsically disordered …
Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system
SD Rao, OA Igoshin - PLoS Computational Biology, 2021 - journals.plos.org
Bacteria use two-component systems (TCSs) to sense environmental conditions and change
gene expression in response to those conditions. To amplify cellular responses, many …
gene expression in response to those conditions. To amplify cellular responses, many …
Protein structure prediction in casp13 using awsem-suite
Recently several techniques have emerged that significantly enhance the quality of
predictions of protein tertiary structures. In this study, we describe the performance of …
predictions of protein tertiary structures. In this study, we describe the performance of …
Forging tools for refining predicted protein structures
Refining predicted protein structures with all-atom molecular dynamics simulations is one
route to producing, entirely by computational means, structural models of proteins that rival …
route to producing, entirely by computational means, structural models of proteins that rival …
[PDF][PDF] Molecular-replacement phasing using predicted protein structures from AWSEM-Suite
The phase problem in X-ray crystallography arises from the fact that only the intensities, and
not the phases, of the diffracting electromagnetic waves are measured directly. Molecular …
not the phases, of the diffracting electromagnetic waves are measured directly. Molecular …
Fibril surface-dependent amyloid precursors revealed by coarse-grained molecular dynamics simulation
YW Ma, TY Lin, MY Tsai - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
Amyloid peptides are known to self-assemble into larger aggregates that are linked to the
pathogenesis of many neurodegenerative disorders. In contrast to primary nucleation, recent …
pathogenesis of many neurodegenerative disorders. In contrast to primary nucleation, recent …