Protein structure homology modeling using SWISS-MODEL workspace

By Lorenza Bordoli, Florian Kiefer, Konstantin Arnold, Pascal Benkert, J. Battey, Torsten Schwede. 2008

1,283 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Toward the estimation of the absolute quality of individual protein structure models (2010, methodology): “Model quality estimates based on the QMEAN scoring function were normalized with respect to the number of interactions.”
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information (2014, background): “Alternatively, a target-template sequence alignment can be specified in the form of a multiple sequence alignment containing the target, the template and eventually other homologous sequences or in the form of a DeepView project file (3,19).”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, methodology): “NIH and National Institute of General Medical Sciences (U01 GM093324-01 to Protein Model Portal and CAMEO); SIB Swiss Institute of Bioinformatics toward the development of CAMEO, SWISS-MODEL, OpenStructure and the operation of the [BC]2 Basel Computational Biology Center.”
State-of-the-Art Estimation of Protein Model Accuracy Using AlphaFold (2022, neutral): “Computational biologists have historically predicted protein structures based on related sequences with experimentally solved structures (11).”
QMEAN server for protein model quality estimation (2009, methodology): “QMEAN can also be used for assessing individual models within SWISS-MODEL Workspace (26,27) together with other tools such as ProQres (28), ANOLEA (29) and WhatCheck (30).”
A Structure-Based Drug Discovery Paradigm (2019, methodology): “There are many other methods for validation of the model [2,31,32].”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “The three-dimensional structure of the barley HvPap-1 protein was modelled by the automated SWISSMODEL program (Bordoli et al., 2009).”
A Review of Deep Learning Methods for Antibodies (2020, background): “While the number of experimentally determined protein crystal structures has grown significantly, it is dwarfed by the amount of sequence data that has been made available [9].”
Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization (2018, methodology): “, 2007) with homology models for Fab 10A (SWISS-MODEL; Arnold et al., 2006; Biasini et al., 2014; Bordoli et al., 2009) as search models and further refined using phenix.”
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, methodology): “It began in the early 1990’s with SWISS-MODEL (5,52)––the first fully automated protein modelling server––and Swiss-PDBviewer (http://spdbv. vital-it.ch, also known as DeepView), an application to align, superimpose, analyse and visualize protein structures.”