Cargando…

Explore Protein Conformational Space With Variational Autoencoder

Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational a...

Descripción completa

Detalles Bibliográficos
Autores principales:	Tian, Hao, Jiang, Xi, Trozzi, Francesco, Xiao, Sian, Larson, Eric C., Tao, Peng
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2021
Materias:	Molecular Biosciences
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8633506/ https://www.ncbi.nlm.nih.gov/pubmed/34869602 http://dx.doi.org/10.3389/fmolb.2021.781635

Ejemplares similares

PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning
por: Xiao, Sian, et al.
Publicado: (2022)

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
por: Kaynak, Burak T., et al.
Publicado: (2022)

DESP: Deep Enhanced Sampling of Proteins’ Conformation Spaces Using AI-Inspired Biasing Forces
por: Salawu, Emmanuel Oluwatobi
Publicado: (2021)

How round is a protein? Exploring protein structures for globularity using conformal mapping
por: Hass, Joel, et al.
Publicado: (2014)

Challenges in predicting stabilizing variations: An exploration
por: Benevenuta, Silvia, et al.
Publicado: (2023)

A Deep Graph Network–Enhanced Sampling Approach to Efficiently Explore the Space of Reduced Representations of Proteins
por: Errica, Federico, et al.
Publicado: (2021)

Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations
por: Mhashal, Anil Ranu, et al.
Publicado: (2022)

Challenges in describing the conformation and dynamics of proteins with ambiguous behavior
por: Roca-Martinez, Joel, et al.
Publicado: (2022)

Understanding protein diffusion on force-induced stretched DNA conformation
por: Mondal, Anupam, et al.
Publicado: (2022)

Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier
por: Orellana, Laura
Publicado: (2019)

Deep learning approaches for conformational flexibility and switching properties in protein design
por: Rudden, Lucas S. P., et al.
Publicado: (2022)

Editorial: Exploring the subcellular proteome and its post-translational modifications
por: Zhang, Shen, et al.
Publicado: (2022)

An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models
por: Parks, Conor, et al.
Publicado: (2020)

Kanamycin-Mediated Conformational Dynamics of Escherichia coli Outer Membrane Protein TolC
por: Pattanayak, Biraja S., et al.
Publicado: (2021)

Electron Transfer Coupled to Conformational Dynamics in Cell Respiration
por: Reidelbach, Marco, et al.
Publicado: (2021)

Accelerating GPCR Drug Discovery With Conformation-Stabilizing VHHs
por: Laeremans, Toon, et al.
Publicado: (2022)

Phosphorylation Induced Conformational Transitions in DNA Polymerase β
por: Srivastava, Amit, et al.
Publicado: (2022)

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
por: Devaurs, Didier, et al.
Publicado: (2017)

Enhancing response of a protein conformational switch by using two disordered ligand binding domains
por: Sekhon, Harsimranjit, et al.
Publicado: (2023)

NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules
por: Sha, Congzhou M., et al.
Publicado: (2022)

Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level
por: Millar, David P.
Publicado: (2022)

Protein Translocation into the Intermembrane Space and Matrix of Mitochondria: Mechanisms and Driving Forces
por: Backes, Sandra, et al.
Publicado: (2017)

The conformation of enkephalin bound to its receptor: an “elusive goal” becoming reality
por: Sanfelice, Domenico, et al.
Publicado: (2014)

Big Data analytics for improved prediction of ligand binding and conformational selection
por: Gupta, Shivangi, et al.
Publicado: (2023)

Exploration of a Robust and Prognostic Immune Related Gene Signature for Cervical Squamous Cell Carcinoma
por: Zuo, Zhihua, et al.
Publicado: (2021)

The Hypervariable Loops of Free TCRs Sample Multiple Distinct Metastable Conformations in Solution
por: Crooks, James E., et al.
Publicado: (2018)

The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor
por: Shi, Yuxin, et al.
Publicado: (2022)

Pinpointing Cell Identity in Time and Space
por: Savulescu, Anca F., et al.
Publicado: (2020)

A Thermodynamic Model for Interpreting Tryptophan Excitation-Energy-Dependent Fluorescence Spectra Provides Insight Into Protein Conformational Sampling and Stability
por: Kwok, A, et al.
Publicado: (2021)

Differences in conformational dynamics within the Hsp90 chaperone family reveal mechanistic insights
por: Graf, Christian, et al.
Publicado: (2014)

Conformational Rigidity within Plasticity Promotes Differential Target Recognition of Nerve Growth Factor
por: Paoletti, Francesca, et al.
Publicado: (2016)

Conformational selection and induced fit for RNA polymerase and RNA/DNA hybrid backtracked recognition
por: Wu, Jian, et al.
Publicado: (2015)

Structural Perspectives on Extracellular Recognition and Conformational Changes of Several Type-I Transmembrane Receptors
por: Chataigner, Lucas M. P., et al.
Publicado: (2020)

Albumin Alters the Conformational Ensemble of Amyloid-β by Promiscuous Interactions: Implications for Amyloid Inhibition
por: Xie, Huisi, et al.
Publicado: (2021)

How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case
por: Paissoni, Cristina, et al.
Publicado: (2021)

Computational and NMR Conformational Analysis of Galactofuranoside Cycles Presented in Bacterial and Fungal Polysaccharide Antigens
por: Gerbst, Alexey G., et al.
Publicado: (2021)

Developing methods to study conformational changes in RNA crystals using a photocaged ligand
por: Lee, Hyun Kyung, et al.
Publicado: (2022)

Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods
por: Gomes, Gregory-Neal W., et al.
Publicado: (2022)

Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA
por: Makraki, Eleni, et al.
Publicado: (2023)

Mapping OMIM Disease–Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes
por: Savojardo, Castrense, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_bs9ve8k9dels4s94f2pn5afpmh