Modeller: generation and refinement of homology-based protein structure models.

By András Fiser, Andrej Sali. 2003

1,625 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Ben M. Webb
2. Andrej Sali
3. Liam J. McGuffin
4. Min-Yi Shen
5. David Eramian
6. Narayanan Eswar
7. Michael Feig
8. Ursula Pieper

In Molecular Biology

1. Ben M. Webb
2. Andrej Sali
3. Liam J. McGuffin
4. Min-Yi Shen
5. David Eramian
6. Narayanan Eswar
7. Alexandre M. J. J. Bonvin
8. Torsten Schwede

Citations in the corpus

• Physics Based Protein Structure Refinement through Multiple Molecular Dynamics Trajectories and Structure Averaging (2013, background): “6,9,12,13 The resulting models are often overall correct, but deviate from experimental structures in detail with typical root-mean-square deviations (RMSDs) of 2–6 A˚ due to intrinsic errors when constructing models based on template structures.”
• The CamSol method of rational design of protein mutants with enhanced solubility. (2015, methodology): “5a, we show the structures of the mutational variants calculated by homology modeling using Modeller [55,56] (see Materials and Methods).”
• Structure, mechanism, and inhibition of Hedgehog acyltransferase (2021, neutral): “…Michaud-Agrawal et al., 2011 https://www.mdanalysis.org GROMACS Hess et al., 2008 www.gromacs.org Modeler Fiser and Sali, 2003 https://salilab.org/modeller/ Martini 2.2 de Jong et al., 2013 http://cgmartini.nl/ Python 3.6 Open Source software…”
• Improvement of 3D protein models using multiple templates guided by single-template model quality assessment (2012, methodology): “8 (Fiser and Sali, 2003) was subsequently used to generate multi-template models using the default parameters and scripts.”
• Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “ModLoop ( http://salilab.org/modloop/ ; Fiser and Sali, 2003b) takes as input a protein structure and one or more residue ranges.”
• Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “ModLoop (http://salilab.org/modloop/; Fiser and Sali, 2003b) takes as input a protein structure and one or more residue ranges.”
• Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “The loop-modeling module in MODELLER implements the optimization-based approach (Fiser et al., 2000; Fiser and Sali, 2003b).”
• Comparative Protein Structure Modeling Using Modeller (2006, methodology): “ModLoop ( http://salilab.org/modloop/ ; Fiser and Sali, 2003b) takes as input a protein structure and one or more residue ranges.”
• HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets (2007, methodology): “21–23 We usually presampled within HADDOCK to obtain an ensemble of starting structures.”
• Model preparation in MOLREP and examples of model improvement using X-ray data (2007, methodology): “These include homology modelling (Schwede et al., 2003; Fiser & Sali, 2003) and scanning the possible conformations of the unknown protein using normal-mode analysis (Suhre & Sanejouand, 2004).”
• Ins and outs of AlphaFold2 transmembrane protein structure predictions (2022, methodology): “AtABCG36 (UniProt ACC: Q9XIE2) was homology modeled based on an ABCG2 homodimer structure (PDBID: 6hzm) using Modeller [60].”