Anthony Nicholls

Summary

Affiliation: OpenEye Scientific Software
Country: USA

Publications

  1. doi request reprint Call for Papers: GRC, CADD, and statistics, and all that
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, NM, USA
    J Comput Aided Mol Des 26:1097-9. 2012
  2. doi request reprint The character of molecular modeling
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, NM, USA
    J Comput Aided Mol Des 26:103-5. 2012
  3. pmc Recommendations for evaluation of computational methods
    Ajay N Jain
    University of California San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 22:133-9. 2008
  4. doi request reprint Predicting small-molecule solvation free energies: an informal blind test for computational chemistry
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, New Mexico 87508, USA
    J Med Chem 51:769-79. 2008
  5. pmc Molecular shape and medicinal chemistry: a perspective
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, New Mexico 87508, USA
    J Med Chem 53:3862-86. 2010
  6. pmc What do we know and when do we know it?
    Anthony Nicholls
    OpenEye Scientific Software, Inc, 9D Bisbee Crt, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 22:239-55. 2008
  7. doi request reprint The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization
    Anthony Nicholls
    OpenEye Scientific Software, Inc Santa Fe, New Mexico, USA
    J Phys Chem B 113:4521-32. 2009
  8. doi request reprint Conformer generation with OMEGA: learning from the data set and the analysis of failures
    Paul C D Hawkins
    OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, USA
    J Chem Inf Model 52:2919-36. 2012
  9. ncbi request reprint Electrostatic evaluation of isosteric analogues
    Roger Sayle
    OpenEye Scientific Software, Suite 1107, 3600 Cerrillos Road, Santa Fe, New Mexico 87507, USA
    J Comput Aided Mol Des 20:191-208. 2006
  10. ncbi request reprint Analysis of SM8 and Zap TK calculations and their geometric sensitivity
    Benjamin A Ellingson
    OpenEye Scientific Software, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 24:335-42. 2010

Collaborators

Detail Information

Publications23

  1. doi request reprint Call for Papers: GRC, CADD, and statistics, and all that
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, NM, USA
    J Comput Aided Mol Des 26:1097-9. 2012
    ..Practical methods will be discussed, deeper issues in applying standard approaches addressed and research on successes and failures in other disciplines presented by invited experts...
  2. doi request reprint The character of molecular modeling
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, NM, USA
    J Comput Aided Mol Des 26:103-5. 2012
    ..In doing so it is hard to be optimistic for the future of the field unless a greater commitment is made to basic science...
  3. pmc Recommendations for evaluation of computational methods
    Ajay N Jain
    University of California San Francisco, Box 0128, San Francisco, CA 94143 0128, USA
    J Comput Aided Mol Des 22:133-9. 2008
    ..Here we propose a modest beginning, with recommendations for requirements on statistical reporting, requirements for data sharing, and best practices for benchmark preparation and usage...
  4. doi request reprint Predicting small-molecule solvation free energies: an informal blind test for computational chemistry
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, New Mexico 87508, USA
    J Med Chem 51:769-79. 2008
    ..6 kcal/mol, with the explicit solvent free energy approach yielding somewhat greater accuracy but at greater computational expense. Insights from outliers and suggestions for future prospective challenges of this kind are presented...
  5. pmc Molecular shape and medicinal chemistry: a perspective
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, New Mexico 87508, USA
    J Med Chem 53:3862-86. 2010
    ..We cannot know what new application to the design and discovery of pharmaceuticals may yet arise from the simple concept of molecular shape, but it is fair to say that the progress so far is impressive...
  6. pmc What do we know and when do we know it?
    Anthony Nicholls
    OpenEye Scientific Software, Inc, 9D Bisbee Crt, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 22:239-55. 2008
    ..Taken together these suggest the modeling field has a long way to go to provide effective assessment of its approaches, either to itself or to a broader audience, but that there are no technical reasons why progress cannot be made...
  7. doi request reprint The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization
    Anthony Nicholls
    OpenEye Scientific Software, Inc Santa Fe, New Mexico, USA
    J Phys Chem B 113:4521-32. 2009
    ....
  8. doi request reprint Conformer generation with OMEGA: learning from the data set and the analysis of failures
    Paul C D Hawkins
    OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, USA
    J Chem Inf Model 52:2919-36. 2012
    ....
  9. ncbi request reprint Electrostatic evaluation of isosteric analogues
    Roger Sayle
    OpenEye Scientific Software, Suite 1107, 3600 Cerrillos Road, Santa Fe, New Mexico 87507, USA
    J Comput Aided Mol Des 20:191-208. 2006
    ....
  10. ncbi request reprint Analysis of SM8 and Zap TK calculations and their geometric sensitivity
    Benjamin A Ellingson
    OpenEye Scientific Software, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 24:335-42. 2010
    ..It is shown that increasing levels of gas phase geometry optimization yield increasingly unfavorable solvation energy for single conformer models...
  11. doi request reprint Essential considerations for using protein-ligand structures in drug discovery
    Gregory L Warren
    OpenEye Scientific Software, Inc, Santa Fe, NM 87508, USA
    Drug Discov Today 17:1270-81. 2012
    ..This process resulted in Iridium, a highly trustworthy protein-ligand structure database to be used for development and validation of structure-based design tools for drug discovery...
  12. ncbi request reprint Gaussian docking functions
    Mark R McGann
    Open Eye Scientific Software, Santa Fe, NM 87501, USA
    Biopolymers 68:76-90. 2003
    ..This implies that this scoring function is not limited to more accurate x-ray structures, as is the case for many of the conventional docking methods, but could be extended to homology models...
  13. ncbi request reprint SAMPL2 and continuum modeling
    Anthony Nicholls
    OpenEye Scientific Software Inc, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 24:293-306. 2010
    ..The results strongly suggest the need for new and repeated experimental measurements, both to clarify what appears to be experimental discrepancies in older measurements and to advance the field in a statistically sound manner...
  14. ncbi request reprint Comparison of shape-matching and docking as virtual screening tools
    Paul C D Hawkins
    OpenEye Scientific Software, Santa Fe, New Mexico 87507, USA
    J Med Chem 50:74-82. 2007
    ..The results show that a shape-based, ligand-centric approach is more consistent than, and often superior to, the protein-centric approach taken by docking...
  15. ncbi request reprint The SAMPL2 blind prediction challenge: introduction and overview
    Matthew T Geballe
    OpenEye Scientific Software Inc, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 24:259-79. 2010
    ..The results of this blind assessment of the state of the field for transfer energy and tautomer ratio prediction both indicate where the field is performing well and point out flaws in current methods...
  16. pmc Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK
    Benjamin A Ellingson
    OpenEye Scientific Sofware, 9 Bisbee Court, Suite D, Santa Fe, NM, 87508, USA
    J Comput Aided Mol Des 28:289-98. 2014
    ..5-2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors. ..
  17. ncbi request reprint Molecular shape and electrostatics in the encoding of relevant chemical information
    Anthony Nicholls
    OpenEye Scientific Software, Inc, 3600 Cerrillos Rd Suite 1107, Santa Fe, NM 87507, USA
    J Comput Aided Mol Des 19:661-86. 2005
    ..We provide methods and evidence to support the conclusion that a useful encoding is practical and propose tests for falsification...
  18. pmc How to do an evaluation: pitfalls and traps
    Paul C D Hawkins
    OpenEye Scientific Software, 9, Bisbee Court, Suite D, Santa Fe, NM 87508, USA
    J Comput Aided Mol Des 22:179-90. 2008
    ....
  19. doi request reprint Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values
    J Michael Word
    OpenEye Scientific Software, Inc, Santa Fe, New Mexico 87508, USA
    Proteins 79:3400-9. 2011
    ....
  20. doi request reprint What do we know?: simple statistical techniques that help
    Anthony Nicholls
    OpenEye Scientific Software, Santa Fe, NM, USA
    Methods Mol Biol 672:531-81. 2011
    ..I present here some basic approaches that have proved useful in my own work, along with examples drawn from the field. In particular, the statistics of evaluations of virtual screening are carefully considered...
  21. ncbi request reprint Variable selection and model validation of 2D and 3D molecular descriptors
    Anthony Nicholls
    OpenEye Scientific Software, Inc, Santa Fe, NM 87507, USA
    J Comput Aided Mol Des 18:451-74. 2004
    ..Additionally, we show an effective methodology using the variables in hypothesis generation; namely, when the crystal structure of a bound ligand is not known...
  22. ncbi request reprint A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
    Thomas S Rush
    Department of Chemical and Screening Sciences, Wyeth Research, 87 Cambridge Park Drive, Cambridge, MA 02140, USA
    J Med Chem 48:1489-95. 2005
    ..These experimental results validate this use of ROCS for chemotype switching or "lead hopping" and suggest that it is of general interest for lead identification in drug discovery endeavors...
  23. ncbi request reprint Lingos, finite state machines, and fast similarity searching
    J Andrew Grant
    AstraZeneca Pharmaceuticals, Mereside, Macclesfield, Cheshire SK10 4TF, England
    J Chem Inf Model 46:1912-8. 2006
    ..The accuracy of LINGO is demonstrated to be comparable to that of a path-based fingerprint and offers a simple yet effective method for similarity searching...