Absolute binding free energies for octa-acids and guests in SAMPL5
暂无分享,去创建一个
Chaok Seok | Bernard R. Brooks | Juyong Lee | Jing Huang | Gerhard König | Florentina Tofoleanu | Frank C. Pickard IV | Minkyung Baek | B. Brooks | Chaok Seok | Jing Huang | Juyong Lee | F. Tofoleanu | Gerhard König | M. Baek
[1] New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997 .
[2] David L. Mobley,et al. The SAMPL4 host–guest blind prediction challenge: an overview , 2014, Journal of Computer-Aided Molecular Design.
[3] Ricardo A. Mata,et al. Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies , 2014, Journal of Computer-Aided Molecular Design.
[4] David S. Goodsell,et al. A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..
[5] David L Mobley,et al. Treating entropy and conformational changes in implicit solvent simulations of small molecules. , 2008, The journal of physical chemistry. B.
[6] B. Gibb,et al. Nonmonotonic assembly of a deep-cavity cavitand. , 2011, Journal of the American Chemical Society.
[7] Traian Sulea,et al. Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge , 2014, Journal of Computer-Aided Molecular Design.
[8] Jian Yin,et al. Overview of the SAMPL5 host–guest challenge: Are we doing better? , 2016, Journal of Computer-Aided Molecular Design.
[9] P. C. Hariharan,et al. Accuracy of AH n equilibrium geometries by single determinant molecular orbital theory , 1974 .
[10] Christopher I. Bayly,et al. Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK , 2014, Journal of Computer-Aided Molecular Design.
[11] Corinne L. D. Gibb,et al. Binding of cyclic carboxylates to octa-acid deep-cavity cavitand , 2014, Journal of Computer-Aided Molecular Design.
[12] Michael R. Shirts,et al. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. , 2003, Physical review letters.
[13] Stefan Bruckner,et al. Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration , 2011, J. Comput. Chem..
[14] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[15] Bogdan I. Iorga,et al. Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field , 2014, Journal of Computer-Aided Molecular Design.
[16] Pengyu Y. Ren,et al. Calculation of protein–ligand binding free energy by using a polarizable potential , 2008, Proceedings of the National Academy of Sciences.
[17] J. Donoso,et al. Theoretical pKa calculations with continuum model solvents, alternative protocols to thermodynamic cycles , 2014 .
[18] Deok-Soo Kim,et al. GalaxyDock2: Protein–ligand docking using beta‐complex and global optimization , 2013, J. Comput. Chem..
[19] Wei Jiang,et al. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application , 2013, J. Chem. Inf. Model..
[20] Jonathan W. Essex,et al. Generalized alteration of structure and parameters: A new method for free‐energy perturbations in systems containing flexible degrees of freedom , 1995, J. Comput. Chem..
[21] H. Berendsen,et al. ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS , 1977 .
[22] D. D. Perrin. Dissociation contants of inorganic acids and bases in aqueous solution , 1969 .
[23] B. Roux,et al. Calculation of absolute protein-ligand binding free energy from computer simulations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[24] M. Gilson,et al. The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.
[25] Stefan Bruckner,et al. Unorthodox uses of Bennett's acceptance ratio method , 2009, J. Comput. Chem..
[26] J. Guthrie,et al. A blind challenge for computational solvation free energies: introduction and overview. , 2009, The journal of physical chemistry. B.
[27] S. Takada,et al. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction , 2002 .
[28] Hee-Cheon Lee,et al. Carceroisomerism and twistomerism in C4c tetraoxatetrathiahemicarceplexes , 1999 .
[29] T. Straatsma,et al. Separation‐shifted scaling, a new scaling method for Lennard‐Jones interactions in thermodynamic integration , 1994 .
[30] M. Gilson,et al. Calculation of protein-ligand binding affinities. , 2007, Annual review of biophysics and biomolecular structure.
[31] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[32] B. Gibb,et al. C-H...X--R (X = Cl, Br, and I) hydrogen bonds drive the complexation properties of a nanoscale molecular basket. , 2001, Journal of the American Chemical Society.
[33] Jianpeng Ma,et al. CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..
[34] Yuko Okamoto,et al. Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules. , 2009, The Journal of chemical physics.
[35] Stefan Bruckner,et al. Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method , 2011, J. Comput. Chem..
[36] A. Mark,et al. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations , 1994 .
[37] Vanja Majstorovic,et al. Changes in high-molecular weight compounds during beech litter decomposition , 2011 .
[38] Christophe Chipot,et al. Standard binding free energies from computer simulations: What is the best strategy? , 2013, Journal of chemical theory and computation.
[39] Willem Verboom,et al. Calix[4]arene‐Based (Hemi)carcerands and Carceplexes: Synthesis, Functionalization, and Molecular Modeling Study , 1997 .
[40] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[41] K. Dill,et al. Predicting absolute ligand binding free energies to a simple model site. , 2007, Journal of molecular biology.
[42] B. Gibb,et al. Guest binding and orientation within open nanoscale hosts. , 2003, Chemistry.
[43] Michael K. Gilson,et al. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction , 2013, J. Comput. Chem..
[44] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[45] Gerhard König,et al. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes , 2014, Journal of chemical theory and computation.
[46] Chaok Seok,et al. Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies , 2016, J. Chem. Inf. Model..
[47] J. Kirkwood. Statistical Mechanics of Fluid Mixtures , 1935 .
[48] Anthony Nicholls,et al. The SAMPL2 blind prediction challenge: introduction and overview , 2010, J. Comput. Aided Mol. Des..
[49] David L Mobley,et al. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. , 2008, Journal of medicinal chemistry.
[50] Ye Mei,et al. Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4 , 2014, Journal of Computer-Aided Molecular Design.
[51] B. Brooks,et al. Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .
[52] Michael K. Gilson,et al. Blind prediction of host–guest binding affinities: a new SAMPL3 challenge , 2012, Journal of Computer-Aided Molecular Design.
[53] G. Shields,et al. Accurate pK(a) calculations for carboxylic acids using complete basis set and Gaussian-n models combined with CPCM continuum solvation methods. , 2001, Journal of the American Chemical Society.
[54] Stefan Boresch,et al. Absolute Binding Free Energies: A Quantitative Approach for Their Calculation , 2003 .
[55] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[56] Bernard R. Brooks,et al. Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations , 2011, Journal of Computer-Aided Molecular Design.
[57] Peter Politzer,et al. Expansion of the σ-hole concept , 2009, Journal of molecular modeling.
[58] D. Truhlar,et al. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .
[59] Charles H. Bennett,et al. Efficient estimation of free energy differences from Monte Carlo data , 1976 .
[60] David L Mobley,et al. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. , 2009, Journal of chemical theory and computation.
[61] 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..
[62] Jie Zhu,et al. BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge , 2015, Journal of Computer-Aided Molecular Design.
[63] Jooyoung Lee,et al. LigDockCSA: Protein–ligand docking using conformational space annealing , 2011, J. Comput. Chem..
[64] C. Cramer,et al. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. , 2009, The journal of physical chemistry. B.
[65] T. Upton,et al. A deuterated deep-cavity cavitand confirms the importance of C-H...X-R hydrogen bonds in guest binding. , 2006, Chemical communications.
[66] Justin A. Lemkul,et al. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. , 2016, Bioorganic & medicinal chemistry.
[67] Wilfred F van Gunsteren,et al. Free energies of ligand binding for structurally diverse compounds. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[68] K. Dill,et al. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". , 2009, Structure.
[69] Donald G Truhlar,et al. Density functionals with broad applicability in chemistry. , 2008, Accounts of chemical research.
[70] Hisashi Okumura,et al. Hamiltonian replica‐permutation method and its applications to an alanine dipeptide and amyloid‐β(29–42) peptides , 2013, J. Comput. Chem..
[71] Stefan Bruckner,et al. Avoiding the van der Waals endpoint problem using serial atomic insertion , 2011, J. Comput. Chem..