Progress in studying intrinsically disordered proteins with atomistic simulations
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October 2015 |
Precise representation of volume properties of water at one atmosphere
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January 1967 |
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
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September 1995 |
Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment
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April 2010 |
Validation of Molecular Simulation: An Overview of Issues
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December 2017 |
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
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July 2013 |
Barstar Has a Highly Dynamic Hydrophobic Core: Evidence from Molecular Dynamics Simulations and Nuclear Magnetic Resonance Relaxation Data †
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August 1998 |
SHIFTX2: significantly improved protein chemical shift prediction
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March 2011 |
Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides †
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January 2005 |
Structural studies of the engrailed homeodomain
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October 1994 |
How Fast-Folding Proteins Fold
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October 2011 |
Comparison of simple potential functions for simulating liquid water
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July 1983 |
Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins
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August 1993 |
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
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September 2015 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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April 1998 |
Not just your average structures
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July 1996 |
Conformational Preferences Underlying Reduced Activity of a Thermophilic Ribonuclease H
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February 2015 |
Molecular simulations of protein dynamics: new windows on mechanisms in biology
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February 2008 |
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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April 1996 |
Crystal Structures of Engrailed Homeodomain Mutants
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October 2003 |
Markov models of molecular kinetics: Generation and validation
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May 2011 |
Chapter 2 Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations
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book
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January 2009 |
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
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May 2011 |
Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme
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December 1998 |
Vicinal Proton Coupling in Nuclear Magnetic Resonance
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September 1963 |
Protein folding and stability: the pathway of folding of barnase
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June 1993 |
Interatomic Potentials from First-Principles Calculations: The Force-Matching Method
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June 1994 |
Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields
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April 2014 |
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
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April 1996 |
Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3JHNα, in a globular protein
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December 1984 |
How does RNase H recognize a DNA.RNA hybrid?
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December 1991 |
Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
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June 2015 |
Systematic Validation of Protein Force Fields against Experimental Data
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February 2012 |
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
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May 2004 |
Multiple origin usage for DNA replication in sdrA(rnh) mutants of Escherichia coli K-12
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September 1984 |
Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles 1 1Edited by A. R. Fersht
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July 1999 |
The Protein Data Bank
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journal
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January 2000 |
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
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November 2000 |
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
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September 1995 |
Solution structure of a protein denatured state and folding intermediate
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October 2005 |
Unifying features in protein-folding mechanisms
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October 2003 |
Computational Enzyme Design
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March 2013 |
Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution
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February 1992 |
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
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March 2012 |
Structure of the Transition State for Folding of a Protein Derived from Experiment and Simulation
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March 1996 |
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
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journal
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April 1996 |
Atomic-Level Characterization of the Structural Dynamics of Proteins
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October 2010 |
Scalable molecular dynamics with NAMD
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January 2005 |
The Amber biomolecular simulation programs
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January 2005 |
Determination of φ and χ 1 Angles in Proteins from 13 C− 13 C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?
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journal
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July 1997 |
Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution
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June 1997 |
Improved side-chain torsion potentials for the Amber ff99SB protein force field
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journal
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January 2010 |
Identification and Characterization of the Unfolding Transition State of Chymotrypsin Inhibitor 2 by Molecular Dynamics Simulations
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journal
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March 1996 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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journal
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March 1977 |
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer
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SC14: International Conference for High Performance Computing, Networking, Storage and Analysis
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conference
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November 2014 |
Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma
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journal
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January 2016 |
Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field
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journal
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May 2015 |
Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of φ-angles
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February 1991 |
Binding of nucleic acids to E.coli RNase HI observed by NMR and CD spectroscopy
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January 1993 |
Comparison of SARS and NL63 Papain-Like Protease Binding Sites and Binding Site Dynamics: Inhibitor Design Implications
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November 2011 |
Hydrogen bond length and proton NMR chemical shifts in proteins
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September 1983 |
ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces
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January 2010 |
Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H
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journal
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December 2011 |
Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
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October 1998 |
Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2.
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journal
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October 1994 |
Dynamics of folded proteins
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journal
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June 1977 |
Zonal methods for the parallel execution of range-limited N-body simulations
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journal
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January 2007 |
Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
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journal
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March 1998 |
An overview of the Amber biomolecular simulation package: Amber biomolecular simulation package
- Salomon-Ferrer, Romelia; Case, David A.; Walker, Ross C.
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 3, Issue 2
https://doi.org/10.1002/wcms.1121
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September 2012 |
Merck molecular force field. IV. conformational energies and geometries for MMFF94
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journal
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April 1996 |
Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation
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journal
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June 2015 |
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
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August 2004 |
Methods for molecular dynamics simulations of protein folding/unfolding in solution
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journal
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September 2004 |
Comparison of multiple crystal structures with NMR data for engrailed homeodomain
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journal
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February 2008 |
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway
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December 1997 |
A new force field for molecular mechanical simulation of nucleic acids and proteins
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journal
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February 1984 |
SAXS-Guided Metadynamics
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June 2015 |
Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants
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November 2005 |
Insights from molecular dynamics simulations for computational protein design
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January 2017 |
Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
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March 2006 |
A Comparison of Multiscale Methods for the Analysis of Molecular Dynamics Simulations
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February 2012 |
Discovery Through the Computational Microscope
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October 2009 |
Molecular dynamics study of enhanced Man5B enzymatic activity
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January 2014 |
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
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April 1996 |
Potential energy functions
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April 1995 |
BioMagResBank
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journal
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December 2007 |
Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate 1 1Edited by A. R. Fersht
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journal
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January 1998 |
Critical Assessment of Current Force Fields. Short Peptide Test Case
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December 2012 |
Re-Engineered p53 Chimera with Enhanced Homo-Oligomerization That Maintains Tumor Suppressor Activity
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February 2014 |
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
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October 1992 |
Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics: Microsecond Simulations of Mdm2
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journal
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July 2015 |
Assignments of backbone proton, carbon-13, and nitrogen-15 resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopy
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journal
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June 1991 |
Analysis of .vphi. and .chi.1 torsion angles for hen lysozyme in solution from proton NMR spin-spin coupling constants
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journal
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January 1991 |
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice: Molecular Dynamics of Crystal Lysozyme
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journal
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June 2015 |
The role of ribonuclease H in multicopy single-stranded DNA synthesis in retron-Ec73 and retron-Ec107 of Escherichia coli
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January 1995 |
The complete folding pathway of a protein from nanoseconds to microseconds
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February 2003 |
Evidence that discontinuous DNA replication in Escherichia coli is primed by approximately 10 to 12 residues of RNA starting with a purine
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July 1985 |
Parallel replica method for dynamics of infrequent events
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journal
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June 1998 |
Combinedab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds
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journal
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December 2001 |
A flexible algorithm for calculating pair interactions on SIMD architectures
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journal
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December 2013 |
Importance of the positive charge cluster in Escherichia coli ribonuclease HI for the effective binding of the substrate
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June 1991 |