The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Comparative Protein Structure Modeling Using MODELLER
Open accessAbstract
Comparative protein structure modeling predicts the three‐dimensional 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 how to use the ModBase database of such models, 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. © 2016 by John Wiley & Sons, Inc.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Wiederstein, M., & Sippl, M. J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm290 · Cited by 5,909
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
Self-citationHHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2012) · Nature Methods · doi:10.1038/nmeth.1818 · Cited by 2,288
Zhou, H., & Zhou, Y. (2002) · Protein Science · doi:10.1110/ps.0217002 · Cited by 902 · cited 5×
“template was used for the modeling. correct equivalences, that is, They include VERIFY3D (Luthy et al., 1992), Prosa2003 (Sippl, 1993; Wiederstein and Sippl, 2007), HARMONY (Topham et al., 1994), ANOLEA (Melo and Feytmans, 1998), DFIRE (Zhou and Zhou, 2002), DOPE (Shen and Sali, 2006), SOAP (Dong et al., 2013), QMEAN…”
InfluentialComparison 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 1×
“…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).”
Srinivasan, N., & Blundell, T. L. (1993) · "Protein Engineering, Design and Selection" · doi:10.1093/protein/6.5.501 · Cited by 119
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Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen
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Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins
Xiao, K., Zhai, J., Feng, Y., Zhou, N., Zhang, X., Zou, J.-J., Li, N., Guo, Y., Li, X., Shen, X., et al. (2020) · Nature · doi:10.1038/s41586-020-2313-x · Cited by 728
SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses
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A practical guide to large-scale docking
Bender, B. J., Gahbauer, S., Luttens, A., Lyu, J., Webb, C. M., Stein, R. M., Fink, E. A., Balius, T. E., Carlsson, J., Irwin, J. J., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00597-z · Cited by 546
“Common programs used for homology modeling include Modeller 52 , Rosetta 53 , ICM 27 and I-Tasser 54 .”
Method
Metadata
- Authors
- Webb, B., & Sali, A.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2016-06
- Volume
- 54
- Issue
- 1
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W4211196614
- Cited by
- 4,316
- References
- 10
- FWCI
- 136.33
- Type
- journal article
- Language
- en
- Open access
- bronze
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