The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.
暂无分享,去创建一个
Yun-Dong Wu | Fan Jiang | Wei Han | F. Jiang | Yundong Wu | W. Han | Wei Han
[1] Hideaki Fujitani,et al. High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters. , 2009, Journal of chemical theory and computation.
[2] A. Perczel,et al. A conformational comparison of N- and C-protected methionine and N- and C-protected homocysteine , 2003 .
[3] H. Schwalbe,et al. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. , 2007, Journal of the American Chemical Society.
[4] 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.
[5] Matthew T. Eddy,et al. Structure of the Alanine Dipeptide in Condensed Phases Determined by 13C NMR , 2004 .
[6] S. Krimm,et al. New chain conformations of poly(glutamic acid) and polylysine. , 1968, Biopolymers.
[7] Jian Zhang,et al. Folding mechanism of β‐hairpins studied by replica exchange molecular simulations , 2005, Proteins.
[8] Charles L. Brooks,et al. Theoretical study of blocked glycine and alanine peptide analogs , 1991 .
[9] Tyuji Hoshino,et al. Ab initio protein structure prediction with force field parameters derived from water‐phase quantum chemical calculation , 2008, J. Comput. Chem..
[10] P. Nguyen,et al. Quantum-classical description of the amide I vibrational spectrum of trialanine. , 2007, The Journal of chemical physics.
[11] H. Schwalbe,et al. Angular dependence of 1J(Ni,Cα i) and 2J(Ni,Cα (i − 1)) coupling constants measured in J-modulated HSQCs , 2002, Journal of biomolecular NMR.
[12] R. Dror,et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.
[13] R. Brüschweiler,et al. Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins. , 2011, Journal of chemical theory and computation.
[14] Wei Zhang,et al. A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..
[15] Kai Griebenow,et al. Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy. , 2003, Journal of the American Chemical Society.
[16] Alexander D. MacKerell,et al. 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 , 2004, J. Comput. Chem..
[17] Yong Duan,et al. Solvation effects on alanine dipeptide: A MP2/cc‐pVTZ//MP2/6‐31G** study of (Φ, Ψ) energy maps and conformers in the gas phase, ether, and water , 2004, J. Comput. Chem..
[18] H. Schwalbe,et al. NMR Spectroscopic Investigation of ψ Torsion Angle Distribution in Unfolded Ubiquitin from Analysis of 3J(Cα,Cα) Coupling Constants and Cross-Correlated Relaxation Rates , 2000 .
[19] S. Gnanakaran,et al. Validation of an all-atom protein force field: From dipeptides to larger peptides , 2003 .
[20] Modulation of intrinsic phi,psi propensities of amino acids by neighbouring residues in the coil regions of protein structures: NMR analysis and dissection of a beta-hairpin peptide. , 1998, Journal of molecular biology.
[21] Y. Duan,et al. Trends in template/fragment-free protein structure prediction , 2010, Theoretical chemistry accounts.
[22] Amit Choudhary,et al. n→π* Interactions in Proteins , 2010, Nature chemical biology.
[23] Gerrit Groenhof,et al. GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..
[24] H. Dyson,et al. Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.
[25] 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.
[26] M. Gruebele,et al. Computational design and experimental testing of the fastest-folding β-sheet protein. , 2011, Journal of molecular biology.
[27] K N Houk,et al. Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules. , 2005, Journal of chemical theory and computation.
[28] Richard A. Friesner,et al. Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields , 1997 .
[29] S. Grzesiek,et al. Side-chain chi(1) conformations in urea-denatured ubiquitin and protein G from (3)J coupling constants and residual dipolar couplings. , 2010, Journal of the American Chemical Society.
[30] 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.
[31] R. Wade,et al. Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations. , 2006, Journal of chemical theory and computation.
[32] Paul T. Matsudaira,et al. NMR structure of the 35-residue villin headpiece subdomain , 1997, Nature Structural Biology.
[33] H. Schwalbe,et al. Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I' band profiles and NMR scalar coupling constants. , 2010, Journal of the American Chemical Society.
[34] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[35] G. Rose,et al. A simple model for polyproline II structure in unfolded states of alanine‐based peptides , 2002, Protein science : a publication of the Protein Society.
[36] Roland L. Dunbrack,et al. Bayesian statistical analysis of protein side‐chain rotamer preferences , 1997, Protein science : a publication of the Protein Society.
[37] Peter L. Freddolino,et al. Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. , 2008, Biophysical journal.
[38] 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.
[39] 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.
[40] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[41] Dan S. Tawfik,et al. Protein Dynamism and Evolvability , 2009, Science.
[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] Alexander D. MacKerell,et al. Improved treatment of the protein backbone in empirical force fields. , 2004, Journal of the American Chemical Society.
[44] R. Brüschweiler,et al. NMR-based protein potentials. , 2010, Angewandte Chemie.
[45] A. Garcia,et al. Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein , 2010, Proteins.
[46] R. Dror,et al. How Fast-Folding Proteins Fold , 2011, Science.
[47] R. L. Baldwin,et al. Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[48] T. Chouard,et al. Structural biology: Breaking the protein rules , 2011, Nature.
[49] S. Grimme,et al. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.
[50] 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.
[51] Roland L. Dunbrack,et al. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains , 1994, Nature Structural Biology.
[52] Yuko Okamoto,et al. Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations , 2004 .
[53] C. Dobson,et al. Side-chain conformations in an unfolded protein: chi1 distributions in denatured hen lysozyme determined by heteronuclear 13C, 15N NMR spectroscopy. , 1999, Journal of molecular biology.
[54] Sándor Suhai,et al. Theoretical Study of Aqueous N-Acetyl-l-alanine N‘-Methylamide: Structures and Raman, VCD, and ROA Spectra , 1998 .
[55] H. Qian,et al. Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix‐forming propensities , 1999, Proteins.
[56] Pau Bernadó,et al. A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[57] J. Choi,et al. Computational vibrational spectroscopy of peptides and proteins in one and two dimensions. , 2009, Accounts of chemical research.
[58] Joseph A. Bank,et al. Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins , 2022 .
[59] R Schweitzer-Stenner,et al. Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy. , 2001, Journal of the American Chemical Society.
[60] C. Brooks,et al. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. , 2006, Journal of the American Chemical Society.
[61] M. Gaigeot,et al. Unravelling the conformational dynamics of the aqueous alanine dipeptide with first-principle molecular dynamics. , 2009, The journal of physical chemistry. B.
[62] Michael I. Jordan,et al. Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model , 2010, PLoS Comput. Biol..
[63] Kang Chen,et al. Spin relaxation enhancement confirms dominance of extended conformations in short alanine peptides. , 2007, Angewandte Chemie.
[64] A. Tropsha,et al. The “random‐coil” state of proteins: Comparison of database statistics and molecular simulations , 1999, Proteins.
[65] S. Hovmöller,et al. Conformations of amino acids in proteins. , 2002, Acta crystallographica. Section D, Biological crystallography.
[66] M. Karplus,et al. Molecular dynamics and protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[67] T. Measey,et al. The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations , 2007, Proceedings of the National Academy of Sciences.
[68] D. Beratan,et al. Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations. , 2008, Biophysical journal.
[69] Hans Frauenfelder,et al. Dynamics of Proteins , 1982 .
[70] H. Nymeyer. Energy landscape of the trpzip2 peptide. , 2009, The journal of physical chemistry. B.
[71] J. Hofrichter,et al. Sub-microsecond protein folding. , 2006, Journal of molecular biology.
[72] A. Liwo,et al. Further evidence for the absence of polyproline II stretch in the XAO peptide. , 2007, Biophysical journal.
[73] Greg L. Hura,et al. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. , 2004, The Journal of chemical physics.
[74] M. Swindells,et al. Intrinsic φ,ψ propensities of amino acids, derived from the coil regions of known structures , 1995, Nature Structural Biology.
[75] Peter L. Freddolino,et al. Force field bias in protein folding simulations. , 2009, Biophysical journal.
[76] R. L. Baldwin,et al. Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. , 1997, Biochemistry.
[77] Charalampos G. Kalodimos,et al. Protein dynamics and allostery: an NMR view. , 2011, Current opinion in structural biology.
[78] Nicholas C Fitzkee,et al. The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB , 2005, Proteins.
[79] Simona Golic Grdadolnik,et al. Determination of conformational preferences of dipeptides using vibrational spectroscopy. , 2008, The journal of physical chemistry. B.
[80] Shoji Takada,et al. SimFold energy function for de novo protein structure prediction: Consensus with Rosetta , 2005, Proteins.
[81] Lorna J. Smith,et al. Toward a Description of the Conformations of Denatured States of Proteins. Comparison of a Random Coil Model with NMR Measurements , 1996 .
[82] Yongqi Huang,et al. Smoothing molecular interactions: The “kinetic buffer” effect of intrinsically disordered proteins , 2010, Proteins.
[83] Xiaolin Cao,et al. The Structure of Alanine Based Tripeptides in Water and Dimethyl Sulfoxide Probed by Vibrational Spectroscopy , 2003 .
[84] Jeremy M. Berg,et al. Thermodynamic β -sheet propensities measured using a zinc-finger host peptide , 1993, Nature.
[85] Yaohang Li,et al. Backbone statistical potential from local sequence-structure interactions in protein loops. , 2010, The journal of physical chemistry. B.
[86] Lauren Wickstrom,et al. Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. , 2009, Biophysical journal.
[87] Eric J. Sorin,et al. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. , 2005, Biophysical journal.
[88] Junichi Higo,et al. AMBER-based hybrid force field for conformational sampling of polypeptides , 2005 .
[89] George D Rose,et al. Structures, basins, and energies: A deconstruction of the Protein Coil Library , 2008, Protein science : a publication of the Protein Society.
[90] M. Gaigeot. Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations. , 2010, Physical chemistry chemical physics : PCCP.
[91] R. Nussinov,et al. Folding and binding cascades: Dynamic landscapes and population shifts , 2008, Protein science : a publication of the Protein Society.
[92] B. Matthews,et al. Structural basis of amino acid alpha helix propensity. , 1993, Science.
[93] K. Griebenow,et al. The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy. , 2004, Journal of the American Chemical Society.
[94] Bosco K. Ho,et al. The Ramachandran plots of glycine and pre-proline , 2005, BMC Structural Biology.
[95] Abhishek K. Jha,et al. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. , 2005, Biochemistry.
[96] Indrajit Ghosh,et al. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles. , 2010, The journal of physical chemistry. B.
[97] R. L. Baldwin,et al. Helix propensities of the amino acids measured in alanine‐based peptides without helix‐stabilizing side‐chain interactions , 1994, Protein science : a publication of the Protein Society.
[98] M. Karplus. Contact Electron‐Spin Coupling of Nuclear Magnetic Moments , 1959 .
[99] L. Serrano. Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation. , 1995, Journal of molecular biology.
[100] M. Sternberg,et al. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. , 1987, Journal of molecular biology.
[101] R. Sankararamakrishnan,et al. Quantum chemical investigations on intraresidue carbonyl-carbonyl contacts in aspartates of high-resolution protein structures. , 2010, The journal of physical chemistry. B.
[102] R. Raines,et al. An electronic effect on protein structure , 2003, Protein science : a publication of the Protein Society.
[103] M. Vannucci,et al. Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space. , 2008, Journal of molecular biology.
[104] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[105] Eric J. Sorin,et al. Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins , 2010, PloS one.
[106] L Regan,et al. A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. , 1994, Biochemistry.
[107] S. Jang,et al. Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation. , 2007, The Journal of chemical physics.
[108] G. Hummer,et al. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. , 2009, The journal of physical chemistry. B.
[109] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[110] Elad Project,et al. Force field‐dependant structural divergence revealed during long time simulations of Calbindin d9k , 2009, J. Comput. Chem..
[111] J M Thornton,et al. Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. , 1996, Journal of molecular biology.
[112] James C. Weisshaar,et al. Conformational Analysis of Alanine Dipeptide from Dipolar Couplings in a Water-Based Liquid Crystal , 2003 .
[113] M. Gaigeot. Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase. , 2010, Physical chemistry chemical physics : PCCP.
[114] R. Best,et al. Balance between alpha and beta structures in ab initio protein folding. , 2010, The journal of physical chemistry. B.
[115] Jirí Vondrásek,et al. Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study. , 2010, The journal of physical chemistry. B.
[116] M. Levitt. Conformational preferences of amino acids in globular proteins. , 1978, Biochemistry.
[117] Alan Grossfield,et al. Role of solvent in determining conformational preferences of alanine dipeptide in water. , 2004, Journal of the American Chemical Society.
[118] 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.
[119] A. Bax,et al. Determination of φ and χ1 Angles in Proteins from 13C−13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond? , 1997 .
[120] Nevena Todorova,et al. Systematic comparison of empirical forcefields for molecular dynamic simulation of insulin. , 2008, The journal of physical chemistry. B.
[121] R. Schweitzer‐Stenner. Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants. , 2009, The journal of physical chemistry. B.
[122] H. Torii. Time-domain calculations of the infrared and polarized Raman spectra of tetraalanine in aqueous solution. , 2007, The journal of physical chemistry. B.
[123] R. Dror,et al. Systematic Validation of Protein Force Fields against Experimental Data , 2012, PloS one.
[124] Lila M. Gierasch,et al. Sending Signals Dynamically , 2009, Science.
[125] G. T. Fraser,et al. Experimental Studies of Peptide Bonds: Identification of the C7eq Conformation of the Alanine Dipeptide Analog N-Acetyl-Alanine N'-Methylamide from Torsion-Rotation Interactions , 2003 .
[126] 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.
[127] Y. Duan,et al. Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations. , 2009, The Journal of chemical physics.
[128] P. Y. Chou,et al. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. , 1974, Biochemistry.
[129] K. Kopple,et al. Solvent-dependent conformational distributions of some dipeptides , 1980 .
[130] 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 .
[131] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[132] Bosco K. Ho,et al. Revisiting the Ramachandran plot: Hard‐sphere repulsion, electrostatics, and H‐bonding in the α‐helix , 2003, Protein science : a publication of the Protein Society.
[133] Minhaeng Cho,et al. Calculations of intermode coupling constants and simulations of amide I, II, and III vibrational spectra of dipeptides , 2009 .
[134] Shuji Tomoda,et al. Solvent effects on the φ–ψ potential surfaces of glycine and alanine dipeptides studied by PCM and I-PCM methods , 2002 .
[135] Timothy H. Click,et al. Intrinsically Disordered Proteins in a Physics-Based World , 2010, International journal of molecular sciences.
[136] M. Plesset,et al. Note on an Approximation Treatment for Many-Electron Systems , 1934 .
[137] Gerhard Stock,et al. Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular dynamics simulations , 2002 .
[138] Marcos R Betancourt. Knowledge-based potential for the polypeptide backbone. , 2008, The journal of physical chemistry. B.
[139] C. Dobson,et al. The concept of a random coil: Residual structure in peptides and denatured proteins , 1996 .
[140] Pavel Hobza,et al. Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. , 2002, Journal of the American Chemical Society.
[141] R. Srinivasan,et al. A physical basis for protein secondary structure. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[142] A. Perczel,et al. Peptide models XLV: Conformational properties of N‐formyl‐L‐methioninamide and its relevance to methionine in proteins , 2004, Proteins.
[143] Ken A Dill,et al. A test on peptide stability of AMBER force fields with implicit solvation. , 2008, The journal of physical chemistry. B.
[144] L J Smith,et al. Side-chains in native and random coil protein conformations. Analysis of NMR coupling constants and chi1 torsion angle preferences. , 1998, Journal of molecular biology.
[145] Roland L. Dunbrack,et al. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. , 2011, Structure.
[146] Shinya Honda,et al. Crystal structure of a ten-amino acid protein. , 2008, Journal of the American Chemical Society.
[147] A. Gronenborn,et al. Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination. , 2004, Journal of the American Chemical Society.
[148] J. Hermans,et al. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace‐Ala‐Nme and Ace‐Gly‐Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution , 2003, Proteins.
[149] Y. Sugita,et al. Comparisons of force fields for proteins by generalized-ensemble simulations , 2004 .
[150] Y. Okamoto,et al. Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank , 2010 .
[151] Y. Kang. Conformational preferences of non-prolyl and prolyl residues. , 2006, The journal of physical chemistry. B.
[152] I. Fdez. Galván,et al. Study on the conformational equilibrium of the alanine dipeptide in water solution by using the averaged solvent electrostatic potential from molecular dynamics methodology. , 2011, The Journal of chemical physics.
[153] Bert L de Groot,et al. Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes. , 2009, Biophysical journal.
[154] N. Skelton,et al. Tryptophan zippers: Stable, monomeric β-hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[155] L. Kay,et al. Protein dynamics and conformational disorder in molecular recognition , 2009, Journal of molecular recognition : JMR.
[156] A. Amadei,et al. Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. , 2010, Current opinion in structural biology.
[157] K. Griebenow,et al. Conformations of alanine-based peptides in water probed by FTIR, Raman, vibrational circular dichroism, electronic circular dichroism, and NMR spectroscopy. , 2007, Biochemistry.
[158] Minhaeng Cho,et al. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra. , 2008, The Journal of chemical physics.
[159] Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly. , 2010, The journal of physical chemistry. B.
[160] R. Brüschweiler,et al. Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field. , 2007, Journal of chemical theory and computation.
[161] 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.
[162] I. Jákli,et al. Peptide models XXIII. Conformational model for polar side‐chain containing amino acid residues: A comprehensive analysis of RHF, DFT, and MP2 properties of HCO‐L‐SER‐NH2 , 2000 .
[163] Jirí Cerný,et al. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. , 2006, Physical chemistry chemical physics : PCCP.
[164] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[165] R. Longhi,et al. Kinetics of contact formation and end-to-end distance distributions of swollen disordered peptides. , 2009, Biophysical journal.
[166] G. Hummer,et al. Are current molecular dynamics force fields too helical? , 2008, Biophysical journal.
[167] C. Dobson,et al. NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. , 1997, Journal of molecular biology.
[168] Vijay S Pande,et al. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[169] E. Stellwagen,et al. Distribution of Helicity within the Model Peptide Acetyl(AAQAA)3amide , 1994 .
[170] R. Luo,et al. Force field influences in β‐hairpin folding simulations , 2006 .
[171] M. Cho,et al. Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis. , 2010, Chirality.
[172] Ian W. Davis,et al. Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.
[173] Christoph Weise,et al. Do Bridging Water Molecules Dictate the Structure of a Model Dipeptide in Aqueous Solution , 2000 .
[174] Oliver F. Lange,et al. Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. , 2010, Biophysical journal.
[175] V. Barone,et al. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .
[176] P. Tompa. Intrinsically unstructured proteins. , 2002, Trends in biochemical sciences.
[177] Mark E Tuckerman,et al. Enhanced conformational sampling of peptides via reduced side-chain and solvent masses. , 2010, The journal of physical chemistry. B.
[178] V. Uversky. Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes. , 2011, Chemical Society reviews.
[179] J. W. Neidigh,et al. Designing a 20-residue protein , 2002, Nature Structural Biology.
[180] F. Avbelj,et al. Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins. , 2000, Journal of molecular biology.
[181] W. DeGrado,et al. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. , 1990, Science.
[182] B. Erman,et al. Computational basis of knowledge‐based conformational probabilities derived from local‐ and long‐range interactions in proteins , 2006, Proteins.
[183] Kang Chen,et al. Conformation of the backbone in unfolded proteins. , 2006, Chemical reviews.