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Zap TK Publications

Featured Publications

J.M. Word and A. Nicholls, "Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values", Proteins: Structure, Function and Bioinformatics, 2011

A. Nicholls, D.L. Mobley, J.P. Guthrie, J.D. Chodera, C.I. Bayly, M.D. Cooper and V.S. Pande, "Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry", J. Med. Chem., 2008, 51 (4), pp 769-779

S.P. Brown and S.W. Muchmore, "High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing", J. Chem. Inf. Model., 2006, 46 (3), pp 999-1005

N.V. Prabhu, P. Zhu and K.A. Sharp, "Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method", J. Comp. Chem., 2004, 25 (16), pp 2049-2064

G.E. Kellogg, S. Phatak, A. Nicholls and J.A. Grant, "Validation of Poisson-Boltzmann Electrostatic Potential Fields in 3D QSAR: A CoMFA Study on Multiple Datasets", QSAR & Combinatorial Science, 2004, 22 (9-10), pp 959-964

J.A. Grant, B.T. Pickup and A. Nicholls, "A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods", J. Comp. Chem., 2001, 22 (6), pp 608-640

Publications by Date

J.M. Word and A. Nicholls, "Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values", Proteins: Structure, Function and Bioinformatics, 2011

B.A. Ellingson, A.G. Skillman and A. Nicholls, "Analysis of SM8 and Zap TK calculations and their geometric sensitivity", J. Comput. Aided Mol. Des., 2010, 24 (4), pp 335-342

A. Nicholls, S. Wlodek and J.A. Grant, "SAMPL2 and continuum modeling", J. Comput. Aided Mol. Des., 2010, 24 (4), pp 293-306

S.P. Brown and S.W. Muchmore, "High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing", J. Chem. Inf. Model., 2006, 46 (3), pp 999-1005

N.V. Prabhu, P. Zhu and K.A. Sharp, "Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method", J. Comp. Chem., 2004, 25 (16), pp 2049-2064

G.E. Kellogg, S. Phatak, A. Nicholls and J.A. Grant, "Validation of Poisson-Boltzmann Electrostatic Potential Fields in 3D QSAR: A CoMFA Study on Multiple Datasets", QSAR & Combinatorial Science, 2004, 22 (9-10), pp 959-964

J.A. Grant, B.T. Pickup and A. Nicholls, "A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods", J. Comp. Chem., 2001, 22 (6), pp 608-640

Bibliography & Related Publications

J.A. Grant, B.T. Pickup, M.J. Sykes, C.A. Kitchen and A. Nicholls, "A simple formula for dielectric polarisation energies: The Sheffield Solvation Model", Chemical Physics Letters, 2007, 441 (1-3), pp 163-166

D.K. Menyhard and G.M. Keseru, "Protonation state of Asp30 exerts crucial influence over surface loop rearrangements responsible for NO release in nitrophorin 4", FEBS Letters, 2005, 579 (24), pp 5392-5398

M.K. Gilson, A. Rashin, R. Fine and B. Honig, "On the calculation of electrostatic interactions in proteins", J. Mol. Biol., 1985, 184 (3), pp 503-516