I. W. Davis
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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
- I. W. Davis, A. Leaver-Fay, +8 authors D. C. Richardson
- Medicine, Biology
- Nucleic Acids Res.
- 22 April 2007
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric… Expand
Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure… Expand
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid… Expand
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
- I. W. Davis, L. Murray, J. Richardson, D. C. Richardson
- Computer Science, Medicine
- Nucleic Acids Res.
- 1 July 2004
MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis… Expand
Structure Validation by C Geometry: , and C Deviation
Geometrical validation around the C is described, with a new C measure and up- dated Ramachandran plot. Deviation of the ob- served C atom from ideal position provides a single measure encapsulating… Expand
Phenix - a comprehensive python-based system for macromolecular structure solution
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many… Expand
RosettaLigand docking with full ligand and receptor flexibility.
Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and… Expand
KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.
- Vincent B. Chen, I. W. Davis, D. C. Richardson
- Chemistry, Medicine
- Protein science : a publication of the Protein…
- 1 November 2009
Proper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the… Expand
Scientific benchmarks for guiding macromolecular energy function improvement.
Accurate energy functions are critical to macromolecular modeling and design. We describe new tools for identifying inaccuracies in energy functions and guiding their improvement, and illustrate the… Expand