Guide for determination of protein structural ensembles by combining cryo-EM data with metadynamics.
Sign Up to like & getrecommendations! Published in 2022 at "FEBS open bio"
DOI: 10.1002/2211-5463.13542
Abstract: Metadynamics Electron Microscopy MetaInference (MEMMI) is an integrative structural biology method that enables a rapid and accurate characterization of protein structural dynamics at the atomic level and the error in the Cryo-EM experimental data, even… read more here.
Keywords: structural ensembles; microscopy; cryo; protein structural ... See more keywords
β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides.
Sign Up to like & getrecommendations! Published in 2019 at "Biophysical journal"
DOI: 10.1016/j.bpj.2018.12.015
Abstract: Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive… read more here.
Keywords: cyclic hexapeptides; amino acids; well structured; global structural ... See more keywords
CLoNe: Automated clustering based on local density neighborhoods for application to biomolecular structural ensembles.
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa742
Abstract: MOTIVATION Proteins are intrinsically dynamic entities. Flexibility sampling methods, such as molecular dynamics or those arising from integrative modeling strategies are now commonplace and enable the study of molecular conformational landscapes in many contexts. Resulting… read more here.
Keywords: local density; analysis; structural ensembles; ensembles clone ... See more keywords
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad260
Abstract: Abstract RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering… read more here.
Keywords: structural ensembles; ring pymol; residue interaction; ensembles molecular ... See more keywords
Transferable deep generative modeling of intrinsically disordered protein conformations
Sign Up to like & getrecommendations! Published in 2024 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1012144
Abstract: Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. Molecular simulations are… read more here.
Keywords: structural ensembles; intrinsically disordered; disordered protein; model ... See more keywords
Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift
Sign Up to like & getrecommendations! Published in 2021 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2021.766830
Abstract: Monomer dissociation and subsequent misfolding of the transthyretin (TTR) is one of the most critical causative factors of TTR amyloidosis. TTR amyloidosis causes several human diseases, such as senile systemic amyloidosis and familial amyloid cardiomyopathy/polyneuropathy;… read more here.
Keywords: aggregation; aggregation prone; analysis; prone structural ... See more keywords