Computational Chemistry Tools

[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.