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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.
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“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]
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Items 101–126 of 126
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“A search even more focused on the feasible conformations would require the use of database [21] or fragment assembly methods [55, 36], something not considered in this work.”
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Szarecka, A., & Meirovitch, H. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp055771+ · Cited by 7
Watanabe, Y. S., Fukunishi, Y., & Nakamura, H. (2006) · BIOPHYSICS · doi:10.2142/biophysics.2.1 · Cited by 6
Totrov, M. M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-588-6_9 · Cited by 7
Ikeda, K., Hirokawa, T., Higo, J., et al. (2008) · BMC Structural Biology · doi:10.1186/1472-6807-8-37 · Cited by 5
“Some analyses examine short loops with respect to their completeness [27,28] and elaborate classification [26,29].”
BackgroundAlgorithms exploiting the chain structure of proteins
Latombe, J., & Lotan, I. (2004) · Cited by 4
Koehl, P. (2010) · Humana Press eBooks · doi:10.1007/978-1-60327-233-9_1 · Cited by 4
“In 1994, however, John Moult and colleagues concluded that the use of fragments from the PDB to generate loops was useful for loops up to a length of 4 residues, as the completeness of the database degrades rapidly with increasing length [78].”
BackgroundComparative Modeling of Drug Target Proteins
Eswar, N., & Šali, A. (2007) · Elsevier eBooks · doi:10.1016/b0-08-045044-x/00251-0 · Cited by 6
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“As a result, only loops up to 4-7 residues long have most of their conceivable conformations present in the database of known protein structures(Fidelis et al., 1994;Lessel, Schomburg, 1994).”
BackgroundInfluentialHomology-Based Modeling of Protein Structure
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Homology Modeling in Protein Structure Predictions
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Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction
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Protein Structure Prediction From Primary Sequence
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Classification of loops in protein structures: applications on loop modeling and protein function
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Comparing and modeling protein structure
Levitt, M., Guibas, L., & Kolodny, R. (2004)
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
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