Computational Chemistry Tools
暂无分享,去创建一个
Kenyon G. Daniel | Wayne C. Guida | Wesley H. Brooks | Rainer Metcalf | W. Guida | K. Daniel | W. Brooks | Rainer Metcalf
[1] Haruki Nakamura,et al. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..
[2] Jan H. Jensen,et al. Very fast empirical prediction and rationalization of protein pKa values , 2005, Proteins.
[3] G. Hummer,et al. Are current molecular dynamics force fields too helical? , 2008, Biophysical journal.
[4] Hongwei Wang,et al. How cryo‐electron microscopy and X‐ray crystallography complement each other , 2017, Protein science : a publication of the Protein Society.
[5] R. Gargallo,et al. Molecular dynamics simulation of highly charged proteins: Comparison of the particle‐particle particle‐mesh and reaction field methods for the calculation of electrostatic interactions , 2003, Protein science : a publication of the Protein Society.
[6] Matthew P. Repasky,et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.
[7] Anna Tramontano,et al. Evaluation of the template‐based modeling in CASP12 , 2018, Proteins.
[8] M. Head‐Gordon,et al. A fifth-order perturbation comparison of electron correlation theories , 1989 .
[9] E. Paquet,et al. Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review , 2015, BioMed research international.
[10] M. Trsic,et al. Universal gaussian and Slater-type basis sets for atoms He to Ar based on an integral version of the Hartree-Fock equations , 1987 .
[11] Youyong Li,et al. Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. , 2013, The journal of physical chemistry. B.
[12] Tingjun Hou,et al. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking , 2011, J. Comput. Chem..
[13] T. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..
[14] Juan J. de Pablo,et al. Monte Carlo simulation of proteins through a random walk in energy space , 2002 .
[15] Adam Zemla,et al. LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..
[16] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[17] A K Dunker,et al. Comparing predictors of disordered protein. , 2000, Genome informatics. Workshop on Genome Informatics.
[18] K. Ginalski. Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.
[19] Marco Biasini,et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information , 2014, Nucleic Acids Res..
[20] Samuel Genheden,et al. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations. , 2013, Physical chemistry chemical physics : PCCP.
[21] C. Venkatachalam,et al. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.
[22] Donald G. Truhlar,et al. Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields , 2014, Accounts of chemical research.
[23] Michael J. Frisch,et al. Self‐consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets , 1984 .
[24] E. Cino,et al. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations , 2012, Journal of chemical theory and computation.
[25] Dan Li,et al. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power. , 2016, Physical chemistry chemical physics : PCCP.
[26] L. Mirny,et al. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. , 1999, Journal of molecular biology.
[27] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[28] M. DePristo,et al. Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. , 2004, Structure.
[29] William L. Jorgensen,et al. Monte Carlo vs Molecular Dynamics for Conformational Sampling , 1996 .
[30] M. W. van der Kamp,et al. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. , 2013, Biochemistry.
[31] K Fidelis,et al. A large‐scale experiment to assess protein structure prediction methods , 1995, Proteins.
[32] Torsten Schwede,et al. BIOINFORMATICS Bioinformatics Advance Access published November 12, 2005 The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling , 2022 .
[33] Woody Sherman,et al. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field. , 2012, Journal of chemical theory and computation.
[34] I. Kuntz,et al. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. , 1988, Journal of medicinal chemistry.
[35] Michael Levitt,et al. Near-native structure refinement using in vacuo energy minimization , 2007, Proceedings of the National Academy of Sciences.
[36] Philip E. Bourne,et al. The RCSB PDB information portal for structural genomics , 2005, Nucleic Acids Res..
[37] J. Šponer,et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .
[38] L. Grippo,et al. A truncated Newton method with nonmonotone line search for unconstrained optimization , 1989 .
[39] M. Karplus,et al. Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations , 1991, Proteins.
[40] José A. Brito,et al. X-ray Crystallography , 2013 .
[41] G. Vriend,et al. Homology modeling. , 2020, Methods of biochemical analysis.
[42] Max W. Chang,et al. Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina , 2010, PloS one.
[43] M. Head‐Gordon,et al. Analytical second derivatives for excited electronic states using the single excitation configuration interaction method: theory and application to benzo[a]pyrene and chalcone , 1999 .
[44] K. Dill,et al. The Protein-Folding Problem, 50 Years On , 2012, Science.
[45] Jaroslav M. Ilnytskyi,et al. A domain decomposition molecular dynamics program for the simulation of flexible molecules of spherically-symmetrical and nonspherical sites. II. Extension to NVT and NPT ensembles , 2002 .
[46] Gert Vriend,et al. New ways to boost molecular dynamics simulations , 2015, J. Comput. Chem..
[47] P. Tompa,et al. Introducing protein intrinsic disorder. , 2014, Chemical reviews.
[48] Jennifer L. Knight,et al. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. , 2016, Journal of chemical theory and computation.
[49] Samuel Genheden,et al. A QM/MM study of the binding of RAPTA ligands to cathepsin B , 2011, J. Comput. Aided Mol. Des..
[50] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[51] S. Scheres,et al. How cryo-EM is revolutionizing structural biology. , 2015, Trends in biochemical sciences.
[52] 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 .
[53] D. Thirumalai,et al. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. , 1996, Folding & design.
[54] Roger Fletcher,et al. A Rapidly Convergent Descent Method for Minimization , 1963, Comput. J..
[55] Arthur J. Olson,et al. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..
[56] A. V. Duin,et al. ReaxFF: A Reactive Force Field for Hydrocarbons , 2001 .
[57] John P. A. Ioannidis,et al. A manifesto for reproducible science , 2017, Nature Human Behaviour.
[58] Mark Gerstein,et al. Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic , 2002, Proteins.
[59] Richard A. Friesner,et al. Solvent models for protein–ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations , 2001, J. Comput. Chem..
[60] Marcus D. Hanwell,et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform , 2012, Journal of Cheminformatics.
[61] D. Truhlar,et al. Applications and validations of the Minnesota density functionals , 2011 .
[62] Sudhir B. Kylasa,et al. The ReaxFF reactive force-field: development, applications and future directions , 2016 .
[63] Gang Fu,et al. PubChem Substance and Compound databases , 2015, Nucleic Acids Res..
[64] Alexander D. MacKerell,et al. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. , 2010, Journal of chemical theory and computation.
[65] Martin Head-Gordon,et al. Two-body coupled cluster expansions , 2001 .
[66] Katharina Wendler,et al. Force fields for studying the structure and dynamics of ionic liquids: a critical review of recent developments. , 2012, Chemphyschem : a European journal of chemical physics and physical chemistry.
[67] Gianluca Pollastri,et al. Structural artifacts in protein-ligand X-ray structures: implications for the development of docking scoring functions. , 2009, Journal of medicinal chemistry.
[68] Georg Kresse,et al. Why does the B3LYP hybrid functional fail for metals? , 2007, The Journal of chemical physics.
[69] R. Bartlett,et al. A full coupled‐cluster singles and doubles model: The inclusion of disconnected triples , 1982 .
[70] Walter Thiel,et al. QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.
[71] Peter V Coveney,et al. On the calculation of equilibrium thermodynamic properties from molecular dynamics. , 2016, Physical chemistry chemical physics : PCCP.
[72] Minoru Saito,et al. Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation , 1994 .
[73] Chris Oostenbrink,et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..
[74] William J. Allen,et al. DOCK 6: Impact of new features and current docking performance , 2015, J. Comput. Chem..
[75] M. Delarue,et al. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[76] Rajendra Kumar,et al. g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations , 2014, J. Chem. Inf. Model..
[77] Rafael C. Bernardi,et al. Enhanced sampling techniques in molecular dynamics simulations of biological systems. , 2015, Biochimica et biophysica acta.
[78] B. Honig,et al. A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.
[79] R. Dror,et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.
[80] John P. Overington,et al. ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..
[81] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[82] Tingjun Hou,et al. Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. , 2014, Physical chemistry chemical physics : PCCP.
[83] Yanli Wang,et al. PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..
[84] M. Plesset,et al. Note on an Approximation Treatment for Many-Electron Systems , 1934 .
[85] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[86] George Papadatos,et al. The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..
[87] Clémence Corminboeuf,et al. Systematic errors in computed alkane energies using B3LYP and other popular DFT functionals. , 2006, Organic letters.
[88] Z. Xiang,et al. On the role of the crystal environment in determining protein side-chain conformations. , 2002, Journal of molecular biology.
[89] Alexander D. MacKerell,et al. Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.
[90] Oliver F. Lange,et al. Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. , 2010, Biophysical journal.
[91] Muhammed Tilahun Muhammed,et al. Homology modeling in drug discovery: Overview, current applications, and future perspectives , 2018, Chemical biology & drug design.
[92] Vijay S. Pande,et al. Effects of long‐range electrostatic forces on simulated protein folding kinetics , 2008, J. Comput. Chem..
[93] Giulio Rastelli,et al. Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA , 2009, J. Comput. Chem..
[94] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[95] Hugh Alan Bruck,et al. Digital image correlation using Newton-Raphson method of partial differential correction , 1989 .
[96] Brian Kuhlman,et al. Advances in protein structure prediction and design , 2019, Nature Reviews Molecular Cell Biology.
[97] Manabu Oumi,et al. A doubles correction to electronic excited states from configuration interaction in the space of single substitutions , 1994 .
[98] Boris Polyak. The conjugate gradient method in extremal problems , 1969 .
[99] M. Head‐Gordon,et al. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements? , 2016, Journal of chemical theory and computation.
[100] Wilfred F. van Gunsteren,et al. A generalized reaction field method for molecular dynamics simulations , 1995 .
[101] Yee Siew Choong,et al. General overview on structure prediction of twilight-zone proteins , 2015, Theoretical Biology and Medical Modelling.
[102] George Papadatos,et al. The ChEMBL database in 2017 , 2016, Nucleic Acids Res..
[103] B. D. Todd,et al. Molecular simulation of dendrimers and their mixtures under shear: comparison of isothermal-isobaric (NpT) and isothermal-isochoric (NVT) ensemble systems. , 2005, The Journal of chemical physics.
[104] F. A. Neugebauer,et al. Electrochemical oxidation and structural changes of 5,6-dihydrobenzo[c]cinnolines , 1996 .
[105] B. Kuhn,et al. Validation and use of the MM-PBSA approach for drug discovery. , 2005, Journal of medicinal chemistry.
[106] Y. Sanejouand,et al. On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins. , 2015, Archives of biochemistry and biophysics.
[107] Alexander D. MacKerell,et al. CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..
[108] Udo Seifert,et al. Thermodynamic uncertainty relation for biomolecular processes. , 2015, Physical review letters.
[109] Pär Söderhjelm,et al. How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations. , 2009, The journal of physical chemistry. A.
[110] Dariusz Plewczynski,et al. Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database , 2011, J. Comput. Chem..
[111] S. Gronert. THE NEED FOR ADDITIONAL DIFFUSE FUNCTIONS IN CALCULATIONS ON SMALL ANIONS : THE G2(DD) APPROACH , 1996 .
[112] Matthew L. Leininger,et al. Is Mo/ller–Plesset perturbation theory a convergent ab initio method? , 2000 .
[113] P. Kollman,et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.