Scholars@Duke publication: MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

Publication , Journal Article

Davis, IW; Leaver-Fay, A; Chen, VB; Block, JN; Kapral, GJ; Wang, X; Murray, LW; Arendall, WB; Snoeyink, J; Richardson, JS; Richardson, DC

Published in: Nucleic Acids Res

July 2007

Published version (DOI) Link to item

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 problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

Duke Scholars

Author Jane Shelby Richardson Biochemistry

Author David C. Richardson Biochemistry

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Published In

Nucleic Acids Res

DOI

10.1093/nar/gkm216

EISSN

1362-4962

Publication Date

July 2007

Volume

Issue

Web Server issue

Start / End Page

W375 / W383

Location

England

Related Subject Headings

User-Computer Interface
Software
Reproducibility of Results
Proteins
Protein Conformation
Nucleic Acids
Nucleic Acid Conformation
Molecular Structure
Models, Molecular
Macromolecular Substances

Citation

APA

Chicago

ICMJE

MLA

NLM

Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., … Richardson, D. C. (2007). MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res, 35(Web Server issue), W375–W383. https://doi.org/10.1093/nar/gkm216

Davis, Ian W., Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, et al. “MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.” Nucleic Acids Res 35, no. Web Server issue (July 2007): W375–83. https://doi.org/10.1093/nar/gkm216.

Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375–83.

Davis, Ian W., et al. “MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.” Nucleic Acids Res, vol. 35, no. Web Server issue, July 2007, pp. W375–83. Pubmed, doi:10.1093/nar/gkm216.

Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375–W383.

Published In

Nucleic Acids Res

DOI

10.1093/nar/gkm216

EISSN

1362-4962

Publication Date

July 2007

Volume

Issue

Web Server issue

Start / End Page

W375 / W383

Location

England

Related Subject Headings

User-Computer Interface
Software
Reproducibility of Results
Proteins
Protein Conformation
Nucleic Acids
Nucleic Acid Conformation
Molecular Structure
Models, Molecular
Macromolecular Substances