MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

By Ian W. Davis, L. Murray, Jane S. Richardson, David C Richardson. Nucleic Acids Res., 2004

1,022 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Physical and Theoretical Chemistry

View Paper: https://www.semanticscholar.org/paper/5ed18e30b0f0d9bc92a2d8e9f9551de3d64bd454

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Paul D. Adams
2. Nigel W. Moriarty
3. Jane S. Richardson
4. David C Richardson
5. G. Murshudov
6. J. Headd
7. Anastassis Perrakis
8. Pavel V. Afonine

In Molecular Biology

1. Paul D. Adams
2. Nigel W. Moriarty
3. Jane S. Richardson
4. David C Richardson
5. Gaetano T. Montelione
6. G. Murshudov
7. Yuanpeng Janet Huang
8. Anastassis Perrakis

In Physical and Theoretical Chemistry

1. Paul Karplus
2. Scott A. Hollingsworth
3. Paul D. Adams
4. Gaetano T. Montelione
5. David C Richardson
6. Jane S. Richardson
7. Ron O. Dror
8. Nigel W. Moriarty

Citations in the corpus

• A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions (2011, neutral): “, 2009) as well as in a number of structure validation methods (Davis et al., 2004).”
• AbPredict 2: A server for accurate and unstrained structure prediction of antibody variable domains (2018, background): “Note that joa(Shirai et al., 2014) and jef(Shirai et al., 2014; Weitzner et al., 2014) use MolProbity scores as a model-selection criterion.”
• Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8 (2016, methodology): “Structure validation was carried out using MolProbity [28].”
• Structure and Dynamics of the M3 Muscarinic Acetylcholine Receptor (2012, methodology): “The quality of the resulting structure was assessed using MolProbit”
• MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, background): “These rotamers are of interest, however, for three reasons: (1) some average v and bond angles have relatively large deviations from ideal (Table II), (2) despite this, these rotamers are significantly more common than other rotamers with similar deviations, and (3) the v distributions for both show”
• MolProbity: More and better reference data for improved all‐atom structure validation (2018, background): “12,57 Its structure modeling and corrections, docking construction, image and movie creation, and of course interactive display can still be done offline by us and others, but Java is nearly dead for the important online display in MolProbity.”
• PDB_REDO: constructive validation, more than just looking for errors (2012, background): “Validation software routines have been available since the early 1990s (Laskowski et al., 1993; Hooft et al., 1996; Davis et al., 2004).”
• Anticodon-like loop-mediated dimerization in the crystal structures of HDV-like CPEB3 ribozymes (2023, methodology): “The refined models were validated with MolProbity (Davis et al. 2004).”
• A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins (2010, methodology): “Given this discrepancy, now instead of using the originally predicted allowed and disallowed regions, Ramachandran plots with regions based on empirical distributions are used to assess the stereochemical quality of solved crystal structures as a part of validation tools such as PROCHECK (8), MOLEMA”