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Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics

https://doi.org/10.1021/ci5003334
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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MCSS functionality maps for a flexible protein
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NMR Characterization of Kinase p38 Dynamics in Free and Ligand‐Bound Forms
inferredcites →https://doi.org/10.1002/anie.201105241openalex-snapshot
Inferential NMR/X‐ray‐Based Structure Determination of a Dibenzo[a,d]cycloheptenone Inhibitor–p38α MAP Kinase Complex in Solution
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Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
inferredcites →https://doi.org/10.1002/prot.21123openalex-snapshot
Comparison of multiple Amber force fields and development of improved protein backbone parameters
inferredcites →https://doi.org/10.1002/prot.22353openalex-snapshot
Conformational dynamics of the EGFR kinase domain reveals structural features involved in activation
inferredcites →https://doi.org/10.1007/bf00124016openalex-snapshot
Local elevation: A method for improving the searching properties of molecular dynamics simulation
inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
inferredcites →https://doi.org/10.1016/0021-9991(77)90121-8openalex-snapshot
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
inferredcites →https://doi.org/10.1016/j.bmc.2010.07.047openalex-snapshot
Insights into MAPK p38α DFG flip mechanism by accelerated molecular dynamics
inferredcites →https://doi.org/10.1016/j.bmcl.2008.02.067openalex-snapshot
Synthesis and SAR of new pyrrolo[2,1-f][1,2,4]triazines as potent p38α MAP kinase inhibitors
inferredcites →https://doi.org/10.1016/j.bmcl.2008.06.028openalex-snapshot
Biphenyl amide p38 kinase inhibitors 4: DFG-in and DFG-out binding modes
inferredcites →https://doi.org/10.1016/j.bpj.2010.01.006openalex-snapshot
Tryptophan as a Molecular Shovel in the Glycosyl Transfer Activity of Trypanosoma cruzi Trans-sialidase
inferredcites →https://doi.org/10.1016/j.bpj.2011.06.043openalex-snapshot
Multiple Replica Repulsion Technique for Efficient Conformational Sampling of Biological Systems
inferredcites →https://doi.org/10.1016/j.bpj.2012.03.031openalex-snapshot
“DFG-Flip” in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop
inferredcites →https://doi.org/10.1016/j.jmb.2006.03.021openalex-snapshot
Computational Sampling of a Cryptic Drug Binding Site in a Protein Receptor: Explicit Solvent Molecular Dynamics and Inhibitor Docking to p38 MAP Kinase
inferredcites →https://doi.org/10.1016/j.jmb.2009.06.005openalex-snapshot
p38α MAP Kinase C-Terminal Domain Binding Pocket Characterized by Crystallographic and Computational Analyses
inferredcites →https://doi.org/10.1016/j.jmgm.2003.12.005openalex-snapshot
MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology
inferredcites →https://doi.org/10.1016/s0006-3495(97)78804-0openalex-snapshot
Molecular dynamics study of unbinding of the avidin-biotin complex
inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot
Replica-exchange molecular dynamics method for protein folding
inferredcites →https://doi.org/10.1021/bi0622221openalex-snapshot
Mutagenesis of p38α MAP Kinase Establishes Key Roles of Phe169 in Function and Structural Dynamics and Reveals a Novel DFG-OUT State
inferredcites →https://doi.org/10.1021/bi301112popenalex-snapshot
Insights into the Activity and Specificity of Trypanosoma cruzi trans-Sialidase from Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/bi802230yopenalex-snapshot
Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study of Trypanosoma cruzi trans-Sialidase and Trypanosoma rangeli Sialidase
inferredcites →https://doi.org/10.1021/ci200168bopenalex-snapshot
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins
inferredcites →https://doi.org/10.1021/ci6002202openalex-snapshot
Use of Amino Acid Composition to Predict Ligand-Binding Sites
inferredcites →https://doi.org/10.1021/ci7004725openalex-snapshot
Active Site Pressurization: A New Tool for Structure-Guided Drug Design and Other Studies of Protein Flexibility
inferredcites →https://doi.org/10.1021/cr040426mopenalex-snapshot
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
inferredcites →https://doi.org/10.1021/ct100060topenalex-snapshot
Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories
inferredcites →https://doi.org/10.1021/j100029a038openalex-snapshot
Homology as a Tool in Optimization Problems: Structure Determination of 2D Heteropolymers
inferredcites →https://doi.org/10.1021/ja210751topenalex-snapshot
The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation
inferredcites →https://doi.org/10.1021/ja806846qopenalex-snapshot
Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
inferredcites →https://doi.org/10.1021/ja972457nopenalex-snapshot
Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose
inferredcites →https://doi.org/10.1021/jm0341913openalex-snapshot
Discovery of a Novel Binding Trench in HIV Integrase
inferredcites →https://doi.org/10.1021/jm049575nopenalex-snapshot
Identification of Novel p38α MAP Kinase Inhibitors Using Fragment-Based Lead Generation
inferredcites →https://doi.org/10.1021/jp0777059openalex-snapshot
Finding Transition Pathways Using the String Method with Swarms of Trajectories
inferredcites →https://doi.org/10.1021/jp204407dopenalex-snapshot
Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
inferredcites →https://doi.org/10.1021/jp9806258openalex-snapshot
SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics
inferredcites →https://doi.org/10.1038/nchembio799openalex-snapshot
Rational design of inhibitors that bind to inactive kinase conformations
inferredcites →https://doi.org/10.1038/ncomms4397openalex-snapshot
Activation pathway of Src kinase reveals intermediate states as targets for drug design
inferredcites →https://doi.org/10.1063/1.1755656openalex-snapshot
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
inferredcites →https://doi.org/10.1063/1.470117openalex-snapshot
A smooth particle mesh Ewald method
inferredcites →https://doi.org/10.1073/pnas.0607656103openalex-snapshot
Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism
inferredcites →https://doi.org/10.1073/pnas.0811223106openalex-snapshot
A conserved protonation-dependent switch controls drug binding in the Abl kinase
inferredcites →https://doi.org/10.1073/pnas.202427399openalex-snapshot
Escaping free-energy minima
inferredcites →https://doi.org/10.1073/pnas.94.6.2327openalex-snapshot
The structure of mitogen-activated protein kinase p38 at 2.1-Å resolution
inferredcites →https://doi.org/10.1088/0034-4885/71/12/126601openalex-snapshot
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
inferredcites →https://doi.org/10.1103/physreve.52.2893openalex-snapshot
Predicting slow structural transitions in macromolecular systems: Conformational flooding
inferredcites →https://doi.org/10.1103/physrevlett.86.4983openalex-snapshot
Mathematical Analysis of Coupled Parallel Simulations
inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00614.xopenalex-snapshot
Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble
inferredcites →https://doi.org/10.1371/journal.pbio.0040144openalex-snapshot
A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cphc.201500524openalex-snapshot
Free Energy Calculations using a Swarm‐Enhanced Sampling Molecular Dynamics Approach
inferred← citeshttps://doi.org/10.1007/s42979-020-0081-1openalex-snapshot
Adaptive Ensemble Biomolecular Applications at Scale
inferred← citeshttps://doi.org/10.1016/j.bpj.2025.10.026openalex-snapshot
Drude polarizable force field for phosphorylated polypeptides and proteins
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00185openalex-snapshot
Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00529openalex-snapshot
Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01204openalex-snapshot
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00657openalex-snapshot
CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space
inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b09841openalex-snapshot
Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/acschembio.5b00555openalex-snapshot
A Proteometric Analysis of Human Kinome: Insight into Discriminant Conformation-dependent Residues
inferred← citeshttps://doi.org/10.1093/nar/gkab920openalex-snapshot
Kincore: a web resource for structural classification of protein kinases and their inhibitors
inferred← citeshttps://doi.org/10.4155/fmc-2016-0098openalex-snapshot
Exploiting Computationally Derived Out-Of-The-Box Protein Conformations for Drug Design
inferred← citeshttps://doi.org/10.4155/fmc.16.9openalex-snapshot
Advanced Molecular Dynamics Simulation Methods for Kinase Drug Discovery
inferred← citeshttps://doi.org/10.70675/1a4f06f0zdfa4z41efza87az70239c45c50copenalex-snapshot
Conception d'un logiciel pour la recherche de nouvelles molécules bioactives
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