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Comparative Protein Structure Modeling Using MODELLER
Abstract
Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an accurate three‐dimensional (3‐D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3‐D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3‐D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. Curr. Protoc. Protein Sci. 50:2.9.1‐2.9.31. © 2007 by John Wiley & Sons, Inc.
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Self-citationA new approach to protein fold recognition
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Zhou, H., & Zhou, Y. (2002) · Protein Science · doi:10.1110/ps.0217002 · Cited by 902 · cited 1×
“They include VERIFY3D (Luthy et al., 1992), PROSAII (Sippl, 1993), HARMONY (Topham et al., 1994), ANOLEA (Melo and Feytmans, 1998), and DFIRE (Zhou and Zhou, 2002).”
MethodComparison of systematic search and database methods for constructing segments of protein structure
Fidelis, K., Stern, P. S., Bacon, D., & Moult, J. (1994) · "Protein Engineering, Design and Selection" · doi:10.1093/protein/7.8.953 · Cited by 126 · cited 3×
“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).”
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Metadata
- Authors
- Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Sali, A.
- Venue
- Current Protocols in Protein Science
- Publisher
- Wiley
- Published
- 2007-11
- Volume
- 50
- Issue
- 1
- Pages
- 2.9.1-2.9.37
- ISSN
- 1934-3655 (ISSN-L)
- 1934-3663
- OpenAlex
- W2883755802
- Cited by
- 2,846
- References
- 10
- FWCI
- 14.85
- Type
- journal article
- Language
- en
- Open access
- closed
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