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Comparison of systematic search and database methods for constructing segments of protein structure

Fidelis, Krzysztof, Stern, Peter S., Bacon, David, Moult, John·1994·"Protein Engineering, Design and Selection"

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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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(1999) · doi:10.1002/(sici)1097-0134(1999)37:3+
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Self-citation
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Background
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Computing Protein Structures from Electron Density Maps: The Missing Fragment Problem
Lotan, I., van den Bedem, H., Deacon, A. M., & Latombe, J. (2005) · Springer tracts in advanced robotics · doi:10.1007/10991541_24 · Cited by 12
“The applicability of this approach was initially limited to loops of length 4 [26], but later work suggested an upper limit of 9 [61].”
Background
Ab initio construction of all-atom loop conformations
Jiang, H., & Blouin, C. (2005) · Journal of Molecular Modeling · doi:10.1007/s00894-005-0030-x · Cited by 12
Detecting local residue environment similarity for recognizing near‐native structure models
Kim, H., & Kihara, D. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24658 · Cited by 11
Computational Modeling of Protein Three-Dimensional Structure: Methods and Resources
Pan, A., Gnanasekar, P., & Chakraborty, S. S. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822312-3.00023-0 · Cited by 13
Comparative Protein Structure Modelling
Fiser, A. (2017) · Springer eBooks · doi:10.1007/978-94-024-1069-3_4 · Cited by 11
Computational Biochemistry of Antibodies and T-Cell Receptors
Novotný, J., & Bajorath, J. (1996) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60490-8 · Cited by 10
Clustering and percolation in protein loop structures
Peng, X., He, J., & Niemi, A. J. (2015) · BMC Structural Biology · doi:10.1186/s12900-015-0049-x · Cited by 8
“The success in loop modelling is also often limited to super-secondary structures where α -helices and β -strands are connected to each other by relatively short twists and turns [16, 17].”
Background
Modeling Protein Structure from its Sequence
Martı́-Renom, M. A., Madhusudhan, M. S., Eswar, N., Pieper, U., Shen, M., Šali, A., Fiser, A., Mirković, N., John, B., & Stuart, A. C. (2003) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0501s03 · Cited by 9
“Even according to the more optimistic estimate, ∼30% and 60% of all the possible 8 and 9 residue loop conformations, respectively, are missing from the database (Fidelis et al., 1994).”
Background
Modeling Loops in Protein Structures
Fernández‐Fuentes, N., & Fiser, A. (2010) · doi:10.1002/9780470882207.ch13 · Cited by 8
3.13 Computational Methods Related to Molecular Structure and Reaction Chemistry of Biomaterials ☆
Farokhirad, S., Bradley, R. P., Sarkar, A., Shih, A., Telesco, S., Liu, Y., Venkatramani, R., Eckmann, D. M., AYYASWAMY, P. S., & Radhakrishnan, R. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803581-8.10216-4 · Cited by 7

Authors: Fidelis, K., Stern, P. S., Bacon, D., & Moult, J.
Affiliations: University of Maryland Biotechnology Institute (US)
ORCID: Fidelis, Krzysztof
Bacon, David
Moult, John
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
DOI: 10.1093/protein/7.8.953
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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Comparison of systematic search and database methods for constructing segments of protein structure

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