| Year |
Citation |
Score |
| 2019 |
Grebner C, Malmerberg E, Shewmaker A, Batista J, Nicholls A, Sadowski J. Virtual screening in the cloud: How big is big enough? Journal of Chemical Information and Modeling. PMID 31682421 DOI: 10.1021/Acs.Jcim.9B00779 |
0.36 |
|
| 2016 |
Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, ... ... Nicholls A, et al. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure (London, England : 1993). 24: 502-8. PMID 27050687 DOI: 10.1016/J.Str.2016.02.017 |
0.316 |
|
| 2016 |
Nicholls A. Statistics in molecular modeling: a summary. Journal of Computer-Aided Molecular Design. 30: 279-80. PMID 27001050 DOI: 10.1007/S10822-016-9907-2 |
0.303 |
|
| 2016 |
Nicholls A. Confidence limits, error bars and method comparison in molecular modeling. Part 2: Comparing methods Journal of Computer-Aided Molecular Design. 30: 103-126. DOI: 10.1007/S10822-016-9904-5 |
0.418 |
|
| 2015 |
McGann M, Nicholls A, Enyedy I. The statistics of virtual screening and lead optimization. Journal of Computer-Aided Molecular Design. 29: 923-6. PMID 26481649 DOI: 10.1007/S10822-015-9861-4 |
0.313 |
|
| 2014 |
Nicholls A. JCAMD special series: Statistics and molecular modeling Journal of Computer-Aided Molecular Design. 28: 885-886. PMID 25080076 DOI: 10.1007/S10822-014-9781-8 |
0.308 |
|
| 2014 |
Nicholls A. Confidence limits, error bars and method comparison in molecular modeling. Part 1: The calculation of confidence intervals Journal of Computer-Aided Molecular Design. 28: 887-918. PMID 24899109 DOI: 10.1007/S10822-014-9753-Z |
0.391 |
|
| 2014 |
Ellingson BA, Geballe MT, Wlodek S, Bayly CI, Skillman AG, Nicholls A. Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK Journal of Computer-Aided Molecular Design. 28: 289-298. PMID 24633516 DOI: 10.1007/S10822-014-9720-8 |
0.381 |
|
| 2012 |
Hawkins PC, Nicholls A. Conformer generation with OMEGA: learning from the data set and the analysis of failures. Journal of Chemical Information and Modeling. 52: 2919-36. PMID 23082786 DOI: 10.1021/Ci300314K |
0.352 |
|
| 2012 |
Nicholls A. Call for Papers: GRC, CADD, and statistics, and all that. Journal of Computer-Aided Molecular Design. 26: 1097-9. PMID 23053739 DOI: 10.1007/S10822-012-9613-7 |
0.361 |
|
| 2012 |
Warren GL, Do TD, Kelley BP, Nicholls A, Warren SD. Essential considerations for using protein-ligand structures in drug discovery. Drug Discovery Today. 17: 1270-81. PMID 22728777 DOI: 10.1016/J.Drudis.2012.06.011 |
0.546 |
|
| 2011 |
Word JM, Nicholls A. Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values. Proteins. 79: 3400-9. PMID 21661059 DOI: 10.1002/Prot.23079 |
0.306 |
|
| 2011 |
Nicholls A. What do we know?: simple statistical techniques that help. Methods in Molecular Biology (Clifton, N.J.). 672: 531-81. PMID 20838984 DOI: 10.1007/978-1-60761-839-3_22 |
0.349 |
|
| 2010 |
Wlodek S, Skillman AG, Nicholls A. Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian. Journal of Chemical Theory and Computation. 6: 2140-2152. PMID 26615941 DOI: 10.1021/Ct100095P |
0.367 |
|
| 2010 |
Geballe MT, Skillman AG, Nicholls A, Guthrie JP, Taylor PJ. The SAMPL2 blind prediction challenge: Introduction and overview Journal of Computer-Aided Molecular Design. 24: 259-279. PMID 20455007 DOI: 10.1007/S10822-010-9350-8 |
0.375 |
|
| 2010 |
Ellingson BA, Skillman AG, Nicholls A. Analysis of SM8 and Zap TK calculations and their geometric sensitivity. Journal of Computer-Aided Molecular Design. 24: 335-42. PMID 20432055 DOI: 10.1007/S10822-010-9355-3 |
0.436 |
|
| 2010 |
Nicholls A, Wlodek S, Grant JA. SAMPL2 and continuum modeling. Journal of Computer-Aided Molecular Design. 24: 293-306. PMID 20372975 DOI: 10.1007/S10822-010-9334-8 |
0.428 |
|
| 2010 |
Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B. Molecular shape and medicinal chemistry: a perspective. Journal of Medicinal Chemistry. 53: 3862-86. PMID 20158188 DOI: 10.1021/Jm900818S |
0.599 |
|
| 2009 |
Truchon JF, Nicholls A, Roux B, Iftimie RI, Bayly CI. Integrated Continuum Dielectric Approaches to treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation. Journal of Chemical Theory and Computation. 5: 1785-1802. PMID 24826083 DOI: 10.1021/Ct900029D |
0.358 |
|
| 2009 |
Nicholls A, Wlodek S, Grant JA. The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization. The Journal of Physical Chemistry. B. 113: 4521-32. PMID 19281198 DOI: 10.1021/Jp806855Q |
0.342 |
|
| 2008 |
Truchon JF, Nicholls A, Iftimie RI, Roux B, Bayly CI. Accurate Molecular Polarizabilities Based on Continuum Electrostatics. Journal of Chemical Theory and Computation. 4: 1480-1493. PMID 23646034 DOI: 10.1021/Ct800123C |
0.37 |
|
| 2008 |
Jain AN, Nicholls A. Recommendations for evaluation of computational methods. Journal of Computer-Aided Molecular Design. 22: 133-9. PMID 18338228 DOI: 10.1007/S10822-008-9196-5 |
0.389 |
|
| 2008 |
Nicholls A. What do we know and when do we know it? Journal of Computer-Aided Molecular Design. 22: 239-55. PMID 18253702 DOI: 10.1007/S10822-008-9170-2 |
0.357 |
|
| 2008 |
Hawkins PC, Warren GL, Skillman AG, Nicholls A. How to do an evaluation: pitfalls and traps. Journal of Computer-Aided Molecular Design. 22: 179-90. PMID 18217218 DOI: 10.1007/S10822-007-9166-3 |
0.348 |
|
| 2008 |
Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. Journal of Medicinal Chemistry. 51: 769-79. PMID 18215013 DOI: 10.1021/Jm070549+ |
0.428 |
|
| 2008 |
Hawkins P, Skillman A, Nicholls A. Further adventures in shape space Chemistry Central Journal. 2: 41. DOI: 10.1186/1752-153X-2-S1-P41 |
0.359 |
|
| 2007 |
Grant JA, Pickup BT, Sykes MJ, Kitchen CA, Nicholls A. The Gaussian Generalized Born model: application to small molecules. Physical Chemistry Chemical Physics : Pccp. 9: 4913-22. PMID 17912422 DOI: 10.1039/B707574J |
0.622 |
|
| 2007 |
Hawkins PC, Skillman AG, Nicholls A. Comparison of shape-matching and docking as virtual screening tools. Journal of Medicinal Chemistry. 50: 74-82. PMID 17201411 DOI: 10.1021/Jm0603365 |
0.358 |
|
| 2006 |
Grant JA, Haigh JA, Pickup BT, Nicholls A, Sayle RA. Lingos, finite state machines, and fast similarity searching. Journal of Chemical Information and Modeling. 46: 1912-8. PMID 16995721 DOI: 10.1021/Ci6002152 |
0.602 |
|
| 2006 |
Sayle R, Nicholls A. Electrostatic evaluation of isosteric analogues. Journal of Computer-Aided Molecular Design. 20: 191-208. PMID 16845506 DOI: 10.1007/S10822-006-9045-3 |
0.383 |
|
| 2006 |
Wlodek S, Skillman AG, Nicholls A. Automated ligand placement and refinement with a combined force field and shape potential. Acta Crystallographica Section D-Biological Crystallography. 62: 741-749. PMID 16790930 DOI: 10.1107/S0907444906016076 |
0.366 |
|
| 2006 |
Wlodek S, Skillman AG, Nicholls A. Automated ligand refinement with a combined force field and shape potential Acta Crystallographica Section A. 62: 253-253. DOI: 10.1107/S0108767306094955 |
0.363 |
|
| 2005 |
Nicholls A, Grant JA. Molecular shape and electrostatics in the encoding of relevant chemical information. Journal of Computer-Aided Molecular Design. 19: 661-86. PMID 16328855 DOI: 10.1007/S10822-005-9019-X |
0.344 |
|
| 2005 |
Haigh JA, Pickup BT, Grant JA, Nicholls A. Small molecule shape-fingerprints. Journal of Chemical Information and Modeling. 45: 673-84. PMID 15921457 DOI: 10.1021/Ci049651V |
0.625 |
|
| 2005 |
Rush TS, Grant JA, Mosyak L, Nicholls A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. Journal of Medicinal Chemistry. 48: 1489-95. PMID 15743191 DOI: 10.1021/Jm040163O |
0.37 |
|
| 2004 |
Nicholls A, MacCuish NE, MacCuish JD. Variable selection and model validation of 2D and 3D molecular descriptors. Journal of Computer-Aided Molecular Design. 18: 451-74. PMID 15729846 DOI: 10.1007/S10822-004-5202-8 |
0.309 |
|
| 2003 |
McGann MR, Almond HR, Nicholls A, Grant JA, Brown FK. Gaussian docking functions. Biopolymers. 68: 76-90. PMID 12579581 DOI: 10.1002/Bip.10207 |
0.357 |
|
| 2002 |
Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. Journal of Computational Chemistry. 23: 128-37. PMID 11913378 DOI: 10.1002/Jcc.1161 |
0.391 |
|
| 2001 |
Grant JA, Pickup BT, Nicholls A. A smooth permittivity function for Poisson–Boltzmann solvation methods Journal of Computational Chemistry. 22: 608-640. DOI: 10.1002/Jcc.1032 |
0.65 |
|
| 1995 |
Honig B, Nicholls A. Classical electrostatics in biology and chemistry Science. 268: 1144-1149. PMID 7761829 DOI: 10.1126/Science.7761829 |
0.473 |
|
| 1995 |
Sridharan S, Nicholls A, Sharp KA. A rapid method for calculating derivatives of solvent accessible surface areas of molecules Journal of Computational Chemistry. 16: 1038-1044. DOI: 10.1002/Jcc.540160810 |
0.348 |
|
| 1995 |
Bharadwaj R, Windemuth A, Sridharan S, Honig B, Nicholls A. The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems Journal of Computational Chemistry. 16: 898-913. DOI: 10.1002/Jcc.540160707 |
0.358 |
|
| 1994 |
Tannor DJ, Marten B, Murphy R, Friesner RA, Sitkoff D, Nicholls A, Honig B, Ringnalda M, Goddard WA. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory Journal of the American Chemical Society. 116: 11875-11882. DOI: 10.1021/Ja00105A030 |
0.306 |
|
| 1991 |
Sharp KA, Nicholls A, Friedman R, Honig B. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry. 30: 9686-9697. PMID 1911756 DOI: 10.1021/Bi00104A017 |
0.332 |
|
| 1991 |
Nicholls A, Sharp KA, Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons Proteins: Structure, Function and Genetics. 11: 281-296. PMID 1758883 DOI: 10.1002/Prot.340110407 |
0.342 |
|
| 1991 |
Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation Journal of Computational Chemistry. 12: 435-445. DOI: 10.1002/Jcc.540120405 |
0.316 |
|
| Show low-probability matches. |