The DOI matches its Crossref record.
Comparison of systematic search and database methods for constructing segments of protein structure
Abstract
Two principal methods of determining the conformation of short pieces of polypeptide backbone in proteins have been developed: using a database of known structures and systematically generating all conformations. In this paper, we compare the effectiveness of these two techniques. The completeness of the database for segments of different lengths is examined and it is found to contain most conformations for segments seven residues long, but to deteriorate rapidly for longer regions. When the database segment is to be incorporated into the rest of a structure, at least seven residues are required to build four new residues, because of the need to position the segment relative to the rest of the structure. It is found that such positioning using flanking residues results in large errors in the inserted region. We conclude that the database method is currently not effective for comparative modeling, even for short segments. The systematic search procedure is found to generate almost all structures of short segments found in proteins. In contrast to the database method, low root mean square error structures are obtained for a set of trial segments embedded in the rest of a protein structure. Thus, it should be considered the method of choice.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Local conformational restraints also greatly reduce the size of the space45.”
From Critical assessment of methods of protein structure prediction (CASP)—Round XIV (2021) · cites this paper as [45]
Citations
Cited by
Sorted by citations
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
“As a result, only loops up to 4 to 7 residues long have most of their conceivable conformations present in the database of known protein structures (Fidelis et al., 1994; Lessel and Schomburg, 1994).”
Comparative Protein Structure Modeling Using MODELLER
Webb, B., & Šali, A. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.3 · Cited by 4,404
“…database methods are limited because the number of possible conformations increases exponentially with the length of a loop, and until the late 1990s only loops up to 7 residues long could be modeled using the database of known protein structures (Fidelis et al., 1994; Lessel and Schomburg, 1994).”
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
“Consequently, only segments of 7 residues or less have most of their conceivable conformations present in the database of known protein structures (48).”
BackgroundComparative 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
“Correspondingly, the average model accuracy increased from 43% to 54% (the model accuracy was measured as the percentage of the C α atoms of the model that were within 5 ◦ A of the corresponding C α atoms in the superimposed native structure).”
BackgroundModeling of loops in protein structures
Fiser, A., Do, R. K. G., & Šali, A. (2000) · Protein Science · doi:10.1110/ps.9.9.1753 · Cited by 2,116
Metadata
- Authors
- Fidelis, K., Stern, P. S., Bacon, D., & Moult, J.
- Affiliations
- University of Maryland Biotechnology Institute (US)
- Venue
- "Protein Engineering, Design and Selection"
- Publisher
- Oxford University Press (OUP)
- Published
- 1994
- Volume
- 7
- Issue
- 8
- Pages
- 953-960
- ISSN
- 0269-2139 (ISSN-L)
- 1741-0126
- 1741-0134
- OpenAlex
- W1990698302
- Cited by
- 126
- References
- 0
- Citations by year
- 2025: 1 · 2021: 2 · 2017: 4 · 2016: 2 · 2015: 1 · 2014: 4 · 2013: 1 · 2012: 4
- FWCI
- 2.02
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Protein Engineering Design and Selection (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01lm005102-03, 5r01gm041034-10)
- National Institute of General Medical Sciences (GM41034)
- U.S. National Library of Medicine (LM05102)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
- Keywords
- protein structure comparison, conformational space, structure database, comparative protein modeling, root mean square error
- MeSH terms
- Computer Simulation, Models, Molecular, Peptide Fragments, Databases, Factual, Sequence Alignment, Protein Structure, Secondary
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
