Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …
fields, enables researchers to investigate biological systems at the molecular level with …
DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
While significant advances have been made in predicting static protein structures, the
inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein …
inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein …
Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation
Despite the great promise of genetic code expansion technology to modulate structures and
functions of proteins, external addition of ncAAs is required in most cases and it often limits …
functions of proteins, external addition of ncAAs is required in most cases and it often limits …
Local energetic frustration conservation in protein families and superfamilies
Energetic local frustration offers a biophysical perspective to interpret the effects of
sequence variability on protein families. Here we present a methodology to analyze local …
sequence variability on protein families. Here we present a methodology to analyze local …
[HTML][HTML] Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding
Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions
of proteins in atomistic detail. However, the accuracy of models derived from simulations …
of proteins in atomistic detail. However, the accuracy of models derived from simulations …
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 …
Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA
Bacteriophage T7 gp4 helicase has served as a model system for understanding
mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how …
mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how …
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 …
Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model
Heme is an active center in many proteins. Here we explore computationally the role of
heme in protein folding and protein structure. We model heme proteins using a hybrid model …
heme in protein folding and protein structure. We model heme proteins using a hybrid model …