Residue-specific force field based on protein coil library. RSFF2: modification of AMBER ff99SB.
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[1] Diwakar Shukla,et al. To milliseconds and beyond: challenges in the simulation of protein folding. , 2013, Current opinion in structural biology.
[2] J. Mongan,et al. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.
[3] Mihaly Mezei,et al. Polyproline II helix is the preferred conformation for unfolded polyalanine in water , 2004, Proteins.
[4] J. Hofrichter,et al. Sub-microsecond protein folding. , 2006, Journal of molecular biology.
[5] Wilfred F van Gunsteren,et al. Biomolecular modeling: Goals, problems, perspectives. , 2006, Angewandte Chemie.
[6] Kevin Skadron,et al. Binary Interval Search: a scalable algorithm for counting interval intersections , 2013, Bioinform..
[7] Lijiang Yang,et al. A selective integrated tempering method. , 2009, The Journal of chemical physics.
[8] R. L. Baldwin,et al. Populations of the three major backbone conformations in 19 amino acid dipeptides , 2011, Proceedings of the National Academy of Sciences.
[9] Anna Jagielska,et al. A new force field (ECEPP-05) for peptides, proteins, and organic molecules. , 2006, The journal of physical chemistry. B.
[10] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[11] R. Best,et al. Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse. , 2010, The journal of physical chemistry. B.
[12] Yun-Dong Wu,et al. PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification. , 2010, Journal of chemical theory and computation.
[13] Oliver Beckstein,et al. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations , 2011, J. Comput. Chem..
[14] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[15] J. Berg,et al. Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.
[16] Alexander D. MacKerell,et al. Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. , 2012, Biophysical journal.
[17] Michele Parrinello,et al. Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations. , 2011, Journal of chemical theory and computation.
[18] R. Brüschweiler,et al. NMR-based protein potentials. , 2010, Angewandte Chemie.
[19] Abhishek K. Jha,et al. Statistical coil model of the unfolded state: resolving the reconciliation problem. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[20] Ron O. Dror,et al. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations , 2010, The Journal of general physiology.
[21] Abhishek K. Jha,et al. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. , 2005, Biochemistry.
[22] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[23] Karl F Freed,et al. De novo prediction of protein folding pathways and structure using the principle of sequential stabilization , 2012, Proceedings of the National Academy of Sciences.
[24] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[25] Simona Golic Grdadolnik,et al. Determination of conformational preferences of dipeptides using vibrational spectroscopy. , 2008, The journal of physical chemistry. B.
[26] Gert Vriend,et al. Everyday , 2020, Oxford Research Encyclopedia of Literature.
[27] J. P. Grossman,et al. Millisecond-scale molecular dynamics simulations on Anton , 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.
[28] J. W. Neidigh,et al. Designing a 20-residue protein , 2002, Nature Structural Biology.
[29] F. Jiang,et al. Folding of fourteen small proteins with a residue-specific force field and replica-exchange molecular dynamics. , 2014, Journal of the American Chemical Society.
[30] A. Garcia,et al. Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein , 2010, Proteins.
[31] Yun-Dong Wu,et al. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development. , 2013, Physical chemistry chemical physics : PCCP.
[32] A. Laio,et al. Equilibrium free energies from nonequilibrium metadynamics. , 2006, Physical Review Letters.
[33] Kang Chen,et al. Conformation of the backbone in unfolded proteins. , 2006, Chemical reviews.
[34] G. Hummer,et al. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. , 2009, The journal of physical chemistry. B.
[35] N. Skelton,et al. Tryptophan zippers: Stable, monomeric β-hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[36] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[37] Stefano Piana,et al. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. , 2014, Current opinion in structural biology.
[38] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[39] F. Jiang,et al. Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L. , 2014, The journal of physical chemistry. B.
[40] R. Dror,et al. Systematic Validation of Protein Force Fields against Experimental Data , 2012, PloS one.
[41] R. L. Baldwin,et al. Helix propagation and N‐cap propensities of the amino acids measured in alanine‐based peptides in 40 volume percent trifluoroethanol , 1996, Protein science : a publication of the Protein Society.
[42] Yun-Dong Wu,et al. PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides. , 2010, Journal of chemical theory and computation.
[43] Klaus Schulten,et al. Accelerating Molecular Modeling Applications with GPU Computing , 2009 .
[44] V. Muñoz,et al. Folding dynamics and mechanism of β-hairpin formation , 1997, Nature.
[45] K. Lindorff-Larsen,et al. How robust are protein folding simulations with respect to force field parameterization? , 2011, Biophysical journal.
[46] Jacob D. Durrant,et al. Molecular dynamics simulations and drug discovery , 2011, BMC Biology.
[47] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..
[48] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[49] L Serrano,et al. Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. , 1998, Journal of molecular biology.
[50] F. Jiang,et al. Influence of side chain conformations on local conformational features of amino acids and implication for force field development. , 2010, The journal of physical chemistry. B.
[51] Alexander D. MacKerell,et al. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. , 2012, Journal of chemical theory and computation.
[52] Vijay S. Pande,et al. Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..
[53] Zhengshuang Shi,et al. Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scales. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[54] S. Lifson,et al. On the Theory of Helix—Coil Transition in Polypeptides , 1961 .
[55] Lijiang Yang,et al. On the enhanced sampling over energy barriers in molecular dynamics simulations. , 2006, The Journal of chemical physics.
[56] R. Schweitzer‐Stenner,et al. Conformational changes of trialanine induced by direct interactions between alanine residues and alcohols in binary mixtures of water with glycerol and ethanol. , 2011, Journal of the American Chemical Society.
[57] T. Head-Gordon,et al. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. , 2011, Journal of chemical theory and computation.
[58] Martin Karplus,et al. Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy , 1998 .
[59] R. Friesner,et al. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .
[60] R. Dror,et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.
[61] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[62] George D Rose,et al. Polyproline II structure in a sequence of seven alanine residues , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[63] R. L. Baldwin,et al. Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides. , 1997, Biochemistry.
[64] M. Gruebele,et al. Computational design and experimental testing of the fastest-folding β-sheet protein. , 2011, Journal of molecular biology.
[65] Mark E Tuckerman,et al. Enhanced conformational sampling of peptides via reduced side-chain and solvent masses. , 2010, The journal of physical chemistry. B.
[66] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[67] Rhiju Das,et al. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. , 2012, Journal of chemical theory and computation.
[68] S. Honda,et al. Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. , 2000, Journal of molecular biology.
[69] Nir Kalisman,et al. Differentiable, multi‐dimensional, knowledge‐based energy terms for torsion angle probabilities and propensities , 2008, Proteins.
[70] R. L. Baldwin,et al. Intrinsic backbone preferences are fully present in blocked amino acids , 2006, Proceedings of the National Academy of Sciences of the United States of America.