Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK
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Christopher I. Bayly | Anthony Nicholls | Stanislaw Wlodek | Benjamin A. Ellingson | A. Geoffrey Skillman | Matthew T. Geballe | C. Bayly | A. Nicholls | A. Skillman | S. Wlodek
[1] 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.
[2] A. Geoffrey Skillman. SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors , 2012, Journal of Computer-Aided Molecular Design.
[3] Araz Jakalian,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method , 2000 .
[4] David L Mobley,et al. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. , 2008, Journal of medicinal chemistry.
[5] Thomas A. Halgren,et al. Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules , 1996, J. Comput. Chem..
[6] Anthony Nicholls,et al. The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization. , 2009, The journal of physical chemistry. B.
[7] Donald G Truhlar,et al. Charge Model 4 and Intramolecular Charge Polarization. , 2007, Journal of chemical theory and computation.
[8] Brian E. Granger,et al. IPython: A System for Interactive Scientific Computing , 2007, Computing in Science & Engineering.
[9] David L. Mobley,et al. Blind prediction of solvation free energies from the SAMPL4 challenge , 2014, Journal of Computer-Aided Molecular Design.
[10] J. Guthrie,et al. A blind challenge for computational solvation free energies: introduction and overview. , 2009, The journal of physical chemistry. B.
[11] Christopher I. Bayly,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..
[12] J. Andrew Grant,et al. SAMPL2 and continuum modeling , 2010, J. Comput. Aided Mol. Des..
[13] J. Andrew Grant,et al. A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..
[14] Anthony Nicholls,et al. Analysis of SM8 and Zap TK calculations and their geometric sensitivity , 2010, J. Comput. Aided Mol. Des..
[15] Matthew T. Geballe,et al. The SAMPL3 blind prediction challenge: transfer energy overview , 2012, Journal of Computer-Aided Molecular Design.
[16] Shuai Liu,et al. Blind prediction of HIV integrase binding from the SAMPL4 challenge , 2014, Journal of Computer-Aided Molecular Design.
[17] Thomas A. Halgren,et al. Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular. interactions , 1996, J. Comput. Chem..
[18] Thomas A. Halgren. MMFF VI. MMFF94s option for energy minimization studies , 1999, J. Comput. Chem..
[19] Thomas A. Halgren. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..
[20] Anthony Nicholls,et al. SAMPL2 challenge: prediction of solvation energies and tautomer ratios , 2010, J. Comput. Aided Mol. Des..
[21] Lars Sandberg,et al. Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge , 2014, Journal of Computer-Aided Molecular Design.
[22] T. Halgren. MMFF VI. MMFF94s option for energy minimization studies , 1999, J. Comput. Chem..
[23] Benjamin A. Ellingson,et al. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database , 2010, J. Chem. Inf. Model..
[24] Eamonn F. Healy,et al. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .
[25] J. Peter Guthrie,et al. SAMPL4, a blind challenge for computational solvation free energies: the compounds considered , 2014, Journal of Computer-Aided Molecular Design.
[26] Thomas A. Halgren,et al. Merck molecular force field. IV. conformational energies and geometries for MMFF94 , 1996, J. Comput. Chem..
[27] Thomas A. Halgren. Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..
[28] Eric Jones,et al. SciPy: Open Source Scientific Tools for Python , 2001 .
[29] Anthony Nicholls,et al. The SAMPL2 blind prediction challenge: introduction and overview , 2010, J. Comput. Aided Mol. Des..