Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields
暂无分享,去创建一个
Christopher J. Fennell | S. Shanaka Paranahewage | Cassidy S. Gierhart | C. J. Fennell | S. S. Paranahewage
[1] David L. Mobley,et al. Alchemical prediction of hydration free energies for SAMPL , 2012, Journal of Computer-Aided Molecular Design.
[2] Ken A Dill,et al. Simple liquid models with corrected dielectric constants. , 2012, The journal of physical chemistry. B.
[3] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[4] A. Geoffrey Skillman,et al. SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors , 2012, Journal of Computer-Aided Molecular Design.
[5] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[6] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[7] Charles W. Kehoe,et al. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test , 2012, Journal of Computer-Aided Molecular Design.
[8] Berk Hess,et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .
[9] Araz Jakalian,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method , 2000 .
[10] 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..
[11] Jeremy R. Greenwood,et al. Epik: a software program for pKa prediction and protonation state generation for drug-like molecules , 2007, J. Comput. Aided Mol. Des..
[12] W. M. Haynes. CRC Handbook of Chemistry and Physics , 1990 .
[13] David L. Mobley,et al. A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration , 2014, The journal of physical chemistry. B.
[14] R. C. Weast. CRC Handbook of Chemistry and Physics , 1973 .
[15] David L Mobley,et al. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. , 2007, The journal of physical chemistry. B.
[16] Christopher I. Bayly,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..
[17] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[18] David L Mobley,et al. Charge asymmetries in hydration of polar solutes. , 2008, The journal of physical chemistry. B.
[19] Berk Hess,et al. P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.
[20] Gerrit Groenhof,et al. GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..
[21] Justin L. MacCallum,et al. Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field , 2003, J. Comput. Chem..
[22] David L Mobley,et al. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. , 2008, Journal of medicinal chemistry.
[23] Jonah Z. Vilseck,et al. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling. , 2015, Journal of chemical theory and computation.
[24] J. Guthrie,et al. A blind challenge for computational solvation free energies: introduction and overview. , 2009, The journal of physical chemistry. B.
[25] Vijay S Pande,et al. Building Force Fields: An Automatic, Systematic, and Reproducible Approach. , 2014, The journal of physical chemistry letters.
[26] Michael R. Shirts,et al. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins , 2003 .
[27] P. Kollman,et al. Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.
[28] David L. Mobley,et al. Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge , 2016, bioRxiv.
[29] Wim F Vranken,et al. ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.
[30] David L. Mobley,et al. Blind prediction of solvation free energies from the SAMPL4 challenge , 2014, Journal of Computer-Aided Molecular Design.
[31] Anthony Nicholls,et al. The SAMPL2 blind prediction challenge: introduction and overview , 2010, J. Comput. Aided Mol. Des..
[32] W. Sherman,et al. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field. , 2010, Journal of chemical theory and computation.
[33] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[34] K A Dill,et al. Additivity Principles in Biochemistry* , 1997, The Journal of Biological Chemistry.