Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
Published 2022 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
Authors
Keywords
-
Journal
Frontiers in Molecular Biosciences
Volume 9, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2022-02-04
DOI
10.3389/fmolb.2022.832847
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Revealing the activation mechanism of autoinhibited RalF by integrated simulation and experimental approaches
- (2021) Balint Dudas et al. Scientific Reports
- ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution
- (2021) Burak T Kaynak et al. BIOINFORMATICS
- Parameterizing elastic network models to capture the dynamics of proteins
- (2021) Patrice Koehl et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Advances and challenges in time-resolved macromolecular crystallography
- (2021) Gisela Brändén et al. SCIENCE
- Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations
- (2021) Balint Dudas et al. Scientific Reports
- Unexpected Gating Behaviour of an Engineered Potassium Channel Kir
- (2021) Charline Fagnen et al. Frontiers in Molecular Biosciences
- A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit)
- (2020) Mauricio G. S. Costa et al. Journal of Chemical Information and Modeling
- Inhibition of the activity of HIV-1 protease through antibody binding and mutations probed by molecular dynamics simulations
- (2020) Apoorva Badaya et al. Scientific Reports
- New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies
- (2020) Charline Fagnen et al. Scientific Reports
- Scalable molecular dynamics on CPU and GPU architectures with NAMD
- (2020) James C. Phillips et al. JOURNAL OF CHEMICAL PHYSICS
- Unveiling functional motions based on point mutations in biased signaling systems: A normal mode study on nerve growth factor bound to TrkA
- (2020) Pedro Túlio Resende-Lara et al. PLoS One
- Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling
- (2020) Balint Dudas et al. Frontiers in Molecular Biosciences
- Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods
- (2020) James M Krieger et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Adaptability and specificity: how do proteins balance opposing needs to achieve function?
- (2020) Bentley Wingert et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Protein-ligand complexes as constrained dynamical systems
- (2019) Burak T. Kaynak et al. Journal of Chemical Information and Modeling
- Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines
- (2019) D. Thirumalai et al. CHEMICAL REVIEWS
- Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity
- (2019) She Zhang et al. MOLECULAR BIOLOGY AND EVOLUTION
- Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems
- (2019) Zeynep Kurkcuoglu et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior
- (2019) Yan Zhang et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic
- (2018) Vigneshwaran Namasivayam et al. JOURNAL OF MEDICINAL CHEMISTRY
- RESPEC Incorporates Residue Specificity and the Ligand Effect into the Elastic Network Model
- (2017) Burak T. Kaynak et al. JOURNAL OF PHYSICAL CHEMISTRY B
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
- (2017) Peter Eastman et al. PLoS Computational Biology
- Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states
- (2017) Mehmet Tarik Can et al. PLoS One
- ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution
- (2016) Zeynep Kurkcuoglu et al. Journal of Chemical Theory and Computation
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins
- (2016) Zeynep Kurkcuoglu et al. PLoS One
- Ribonuclease H/DNA Polymerase HIV-1 Reverse Transcriptase Dual Inhibitor: Mechanistic Studies on the Allosteric Mode of Action of Isatin-Based Compound RMNC6
- (2016) Angela Corona et al. PLoS One
- The anisotropic network model web server at 2015 (ANM 2.0)
- (2015) E. Eyal et al. BIOINFORMATICS
- How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics
- (2015) Zeynep Kurkcuoglu et al. BIOPHYSICAL JOURNAL
- Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes
- (2015) Nicolas Floquet et al. BIOPHYSICAL JOURNAL
- Adaptability of protein structures to enable functional interactions and evolutionary implications
- (2015) Turkan Haliloglu et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Energy landscape of LeuT from molecular simulations
- (2015) Mert Gur et al. JOURNAL OF CHEMICAL PHYSICS
- Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes
- (2015) Mauricio G. S. Costa et al. Journal of Chemical Theory and Computation
- Evol and ProDy for bridging protein sequence evolution and structural dynamics
- (2014) A. Bakan et al. BIOINFORMATICS
- An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis
- (2014) Zoltan Palmai et al. PLoS Computational Biology
- Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase
- (2013) Mert Gur et al. BIOPHYSICAL JOURNAL
- Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase
- (2013) Zeynep Kurkcuoglu et al. Entropy
- Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions
- (2013) Edvin Fuglebakk et al. Journal of Chemical Theory and Computation
- CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
- (2013) Jing Huang et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- ProDy: Protein Dynamics Inferred from Theory and Experiments
- (2011) A. Bakan et al. BIOINFORMATICS
- A Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase
- (2011) Louiza Zerrad et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening
- (2011) Paulo R. Batista et al. Journal of Chemical Theory and Computation
- Large collective motions regulate the functional properties of glutamate transporter trimers
- (2011) J. Jiang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Global Dynamics of Proteins: Bridging Between Structure and Function
- (2010) Ivet Bahar et al. Annual Review of Biophysics
- Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis
- (2010) Matthew J. Cliff et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structural basis of HIV-1 resistance to AZT by excision
- (2010) Xiongying Tu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy
- (2010) Toshimasa Yamazaki et al. PROTEIN SCIENCE
- Improved side-chain torsion potentials for the Amber ff99SB protein force field
- (2010) Kresten Lindorff-Larsen et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Protein elastic network models and the ranges of cooperativity
- (2009) L. Yang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
- (2009) A. Bakan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: A molecular dynamics study
- (2009) Zoltan Palmai et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Dimerization Affects Collective Dynamics of Triosephosphate Isomerase†
- (2008) Sertan Cansu et al. BIOCHEMISTRY
- Catalytically Requisite Conformational Dynamics in the mRNA-Capping Enzyme Probed by Targeted Molecular Dynamics†
- (2008) Robert V. Swift et al. BIOCHEMISTRY
- CHARMM-GUI: A web-based graphical user interface for CHARMM
- (2008) Sunhwan Jo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started