标题
CHARMM-GUI 10 years for biomolecular modeling and simulation
作者
关键词
-
出版物
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 38, Issue 15, Pages 1114-1124
出版商
Wiley
发表日期
2016-11-17
DOI
10.1002/jcc.24660
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- Molecular dynamics simulation strategies for protein–micelle complexes
- (2016) Xi Cheng et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
- (2016) Takaharu Mori et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors
- (2016) Evan J. Arthur et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein
- (2015) Emilia L. Wu et al. BIOPHYSICAL JOURNAL
- Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes
- (2015) Xi Cheng et al. BIOPHYSICAL JOURNAL
- CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
- (2015) Yifei Qi et al. BIOPHYSICAL JOURNAL
- Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension
- (2015) Mingjun Yang et al. Journal of Chemical Theory and Computation
- Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM)
- (2015) Mingjun Yang et al. Journal of Chemical Theory and Computation
- Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy
- (2015) Hui Sun Lee et al. Journal of Chemical Theory and Computation
- Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations
- (2015) Kira A. Armacost et al. Journal of Chemical Theory and Computation
- CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
- (2015) Yifei Qi et al. Journal of Chemical Theory and Computation
- CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
- (2015) Jumin Lee et al. Journal of Chemical Theory and Computation
- Membrane Environment Modulates the pKa Values of Transmembrane Helices
- (2015) Afra Panahi et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Simulating the Distance Distribution between Spin-Labels Attached to Proteins
- (2015) Shahidul M. Islam et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion
- (2015) Xiancheng Zeng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
- (2015) Jaewoon Jung et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
- (2015) Rong Shen et al. PLoS Computational Biology
- CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations
- (2014) Yifei Qi et al. Journal of Chemical Information and Modeling
- Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent
- (2014) Clément Arnarez et al. Journal of Chemical Theory and Computation
- All-atom polarizable force field for DNA based on the classical drude oscillator model
- (2014) Alexey Savelyev et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations
- (2014) Emilia L. Wu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues
- (2014) Garrett B. Goh et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Carbohydrate–Protein Interactions That Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity
- (2014) Brandon C. Knott et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era
- (2014) Qiang Cui et al. PLoS Computational Biology
- xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
- (2014) Ryan McGreevy et al. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
- Bending Free Energy from Simulation: Correspondence of Planar and Inverse Hexagonal Lipid Phases
- (2013) Alexander J. Sodt et al. BIOPHYSICAL JOURNAL
- Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
- (2013) Emilia L. Wu et al. BIOPHYSICAL JOURNAL
- Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods
- (2013) Dhruva K. Chakravorty et al. JOURNAL OF BIOMOLECULAR NMR
- CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems
- (2013) Xi Cheng et al. Journal of Chemical Information and Modeling
- Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
- (2013) Lei Huang et al. Journal of Chemical Theory and Computation
- pH-Dependent Dynamics of Complex RNA Macromolecules
- (2013) Garrett B. Goh et al. Journal of Chemical Theory and Computation
- Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
- (2013) Pedro E. M. Lopes et al. Journal of Chemical Theory and Computation
- Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
- (2013) Tsjerk A. Wassenaar et al. Journal of Chemical Theory and Computation
- Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron–Electron Resonance Spectroscopy
- (2013) Benoît Roux et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme
- (2013) Shahidul M. Islam et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Chaperone activation by unfolding
- (2013) L. Foit et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability
- (2013) Sean M. Law et al. PROTEIN SCIENCE
- Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism
- (2013) Garrett B. Goh et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Biomolecular Simulation: A Computational Microscope for Molecular Biology
- (2012) Ron O. Dror et al. Annual Review of Biophysics
- MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
- (2012) Adam Hospital et al. BIOINFORMATICS
- Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model
- (2012) Y. Zenmei Ohkubo et al. BIOPHYSICAL JOURNAL
- Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
- (2012) K. Vanommeslaeghe et al. Journal of Chemical Information and Modeling
- Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
- (2012) K. Vanommeslaeghe et al. Journal of Chemical Information and Modeling
- CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
- (2012) Sunhwan Jo et al. Journal of Chemical Information and Modeling
- Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains
- (2012) Wei Han et al. Journal of Chemical Theory and Computation
- Improved Parameters for the Martini Coarse-Grained Protein Force Field
- (2012) Djurre H. de Jong et al. Journal of Chemical Theory and Computation
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
- (2012) Peter Eastman et al. Journal of Chemical Theory and Computation
- Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
- (2012) Robert B. Best et al. Journal of Chemical Theory and Computation
- Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations
- (2012) Wenbo Yu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Brownian Dynamics Simulations of Ion Transport through the VDAC
- (2011) Kyu Il Lee et al. BIOPHYSICAL JOURNAL
- From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
- (2011) Phillip J. Stansfeld et al. Journal of Chemical Theory and Computation
- Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent
- (2011) Garrett B. Goh et al. Journal of Chemical Theory and Computation
- Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies
- (2011) Jennifer L. Knight et al. Journal of Chemical Theory and Computation
- CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling
- (2011) Olgun Guvench et al. Journal of Chemical Theory and Computation
- Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
- (2011) Katarina Hart et al. Journal of Chemical Theory and Computation
- Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins
- (2011) Sunhwan Jo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores
- (2011) Kyu Il Lee et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- MATCH: An atom-typing toolset for molecular mechanics force fields
- (2011) Joseph D. Yesselman et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
- (2011) Elizabeth J. Denning et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- SwissParam: A fast force field generation tool for small organic molecules
- (2011) Vincent Zoete et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- The future of molecular dynamics simulations in drug discovery
- (2011) David W. Borhani et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Probing pH-Dependent Dissociation of HdeA Dimers
- (2011) Bin W. Zhang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments
- (2011) Enguerran Vanquelef et al. NUCLEIC ACIDS RESEARCH
- How Fast-Folding Proteins Fold
- (2011) K. Lindorff-Larsen et al. SCIENCE
- Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids
- (2010) Bob Eisenberg et al. JOURNAL OF CHEMICAL PHYSICS
- Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
- (2010) Wei Jiang et al. Journal of Chemical Theory and Computation
- Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
- (2010) Jeffery B. Klauda et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Polarizable Water Model for the Coarse-Grained MARTINI Force Field
- (2010) Semen O. Yesylevskyy et al. PLoS Computational Biology
- CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
- (2009) Sunhwan Jo et al. BIOPHYSICAL JOURNAL
- Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics
- (2009) Wei Jiang et al. Journal of Chemical Theory and Computation
- Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
- (2009) Xavier Periole et al. Journal of Chemical Theory and Computation
- Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function
- (2009) Wonpil Im et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- CHARMM: The biomolecular simulation program
- (2009) B. R. Brooks et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
- (2009) Yuqing Deng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
- (2009) David L. Mobley et al. STRUCTURE
- CHARMMing: A New, Flexible Web Portal for CHARMM
- (2008) Benjamin T. Miller et al. Journal of Chemical Information and Modeling
- The MARTINI Coarse-Grained Force Field: Extension to Proteins
- (2008) Luca Monticelli et al. Journal of Chemical Theory and Computation
- CHARMM-GUI: A web-based graphical user interface for CHARMM
- (2008) Sunhwan Jo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Application of solid-state NMR restraint potentials in membrane protein modeling
- (2008) Jinhyuk Lee et al. JOURNAL OF MAGNETIC RESONANCE
- Membrane lipids: where they are and how they behave
- (2008) Gerrit van Meer et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- PBEQ-Solver for online visualization of electrostatic potential of biomolecules
- (2008) Sunhwan Jo et al. NUCLEIC ACIDS RESEARCH
- Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
- (2008) Leonardo G. Trabuco et al. STRUCTURE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started