The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
Abstract
The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.
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“Furthermore, the quality of Cn-AMP1 structures was evaluated by analyzing the Ramachandran diagram that is part of the PROCHECK-NMR software [18,25].”
From Structural insights into Cn‐AMP1, a short disulfide‐free multifunctional peptide from green coconut water (2015) · cites this paper as [18]
In the citing paper
“On the basis of Procheck82 analysis of secondary structure elements, the Ramachandran statistics among the top 20 lowest-energy structures are 98% for most favoured regions, 2% for additional allowed regions and 0% for disallowed regions.”
From Predicting multiple conformations via sequence clustering and AlphaFold2 (2024) · cites this paper as [82]
Citations
Cites
PROCHECK: a program to check the stereochemical quality of protein structures
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MOLMOL: A program for display and analysis of macromolecular structures
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X-PLOR Version 3.1: A System for X-ray Crystallography and NMR
Brünger, A. T. (1992) · Medical Entomology and Zoology · Cited by 3,424
Stereochemical quality of protein structure coordinates
Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340120407 · Cited by 1,568
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PostScript Language Reference Manual
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Solution Structure of the HU Protein fromBacillus stearothermophilus
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Self-citationAn Assessment of the Precision and Accuracy of Protein Structures Determined by NMR
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Conformational analysis of protein structures derived from NMR data
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Self-citationNMR structures and methodology
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Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
Comparative Protein Structure Modeling Using Modeller
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2006) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s15 · Cited by 4,618
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Davis, I., Leaver‐Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J. S., Richardson, J. S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm216 · Cited by 3,918
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169
Comparative Protein Structure Modeling Using MODELLER
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2007) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps0209s50 · Cited by 2,874
Metadata
- Authors
- Laskowski, R., Rullmann, J. A., MacArthur, M., Kaptein, R., & Thornton, J.
- Affiliations
- Utrecht University (NL)
- ORCID
- Kaptein, Robert
- Venue
- Journal of Biomolecular NMR
- Published
- 1996-12
- Volume
- 8
- Issue
- 4
- Pages
- 477-86
- ISSN
- 0925-2738 (ISSN-L)
- 1573-5001
- OpenAlex
- W1975459052
- Cited by
- 5,502
- References
- 21
- Citations by year
- 2026: 142 · 2025: 203 · 2024: 205 · 2023: 219 · 2022: 238 · 2021: 204 · 2020: 198 · 2019: 153 · 2018: 130 · 2017: 173 · 2016: 191 · 2015: 194 · 2014: 248 · 2013: 248 · 2012: 233
- FWCI
- 21.02
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Journal of Biomolecular NMR (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- Aqua, protein conformational ensembles
- MeSH terms
- Amino Acid Sequence, Bacterial Proteins, DNA-Binding Proteins, Evaluation Studies as Topic, Models, Molecular, Molecular Sequence Data, Magnetic Resonance Spectroscopy, Proteins, Quality Control, Software, Solutions, Reproducibility of Results, Molecular Structure, Protein Structure, Secondary
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