Comparative protein modelling by satisfaction of spatial restraints.

By Andrej Sali, Tom L. Blundell. 1993

Subfields: Computational Biology & Bioinformatics

How researchers see this paper

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

In Computational Biology & Bioinformatics

1. Yang Zhang
2. Jinbo Xu
3. David Baker
4. Björn Wallner
5. Arne Elofsson
6. Torsten Schwede
7. Sheng Wang
8. Robin Pearce

Citations in the corpus

• Multi-State Modeling of G-protein Coupled Receptors at Experimental Accuracy (2021, neutral): “Finally, as a reference, structure prediction was performed via template-based modeling using MODELLER 31 with the identical structure templates and the sequence alignments used for the AF2 predictions.”
• Protein Sequence Analysis Using the MPI Bioinformatics Toolkit (2020, methodology): “In the following, we show how to use HHpred to select homologous templates of known structure for a query protein and how to extract and subsequently forward their alignment to MODELLER (Sali & Blundell, 1993), a popular program for homology modeling.”
• Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, background): “More recently, the use of multiple templates has seen success in modeling targets in which the sequence identity is below 50% to any given template [10,11].”
• SWISS-MODEL: homology modelling of protein structures and complexes (2018, neutral): “Until recently, the software package ProMod-II (26), using MODELLER (51) as a fall-back, was in use to perform this task.”
• TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “It has been demonstrated else-where (13) that the TM-score has the strongest correlation with the foldability of alignments by the generally used modeling tool, MODELLER (27), in comparison with other similarity scores.”
• Protein structure prediction from sequence variation (2012, methodology): “Many useful and quite accurate three-dimensional models have been computed from amino acid sequences by using the similarity of the protein sequence of interest to another protein whose three-dimensional structure is known, often called template or homology model building 3,4 .”
• The HHpred interactive server for protein homology detection and structure prediction (2005, methodology): “This aligment may be edited by the user and then fed to the MODELLER software (35), accessible via the MPI toolkit for users of HHpred.”
• High resolution comparative modeling with RosettaCM (2013, methodology): “Many excellent methods for comparative modeling have been developed, including the widely used MODELLER program(Eswar et al., 2006; Sali and Blundell, 1993) and, more recently, I-Tasser(Xu et al., 2011) and other methods that explicitly recombine multiple templates.”
• SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information (2014, methodology): “The process typically comprises the following steps: (i) template identification, (ii) template selection, (iii) model building and (iv) model quality estimation (10,11).”
• LOMETS: A local meta-threading-server for protein structure prediction (2007, methodology): “2 (10), where external constraints from LOMETS are incorporated.”
• Evaluation of residue-residue contact predictions in CASP9 (2011, background): “17–20 These are clearly very reliable, but their usefulness is limited to cases where templates can be identified.”
• Multiple conformational states in retrospective virtual screening – homology models vs. crystal structures: beta-2 adrenergic receptor case study (2015, methodology): “For each template, 20 models were generated with Modeller 9v13 software [19] and were evaluated by AUROC in the docking of cluster centroids from actives and true inactives sets (Table 3).”
• The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase (2009, methodology): “MtbSD K69A model was built by restrained-based homology modeling implemented in MODELLER9v1 [ 16 ], with the standard protocol of the comparative protein structure modeling methodology, by satisfaction of spatial restrains [17,18].”
• Interactome3D: adding structural details to protein networks (2013, methodology): “Modeling is performed with Modeller 28 using the protocol described above.”
• Modern homology modeling of G-protein coupled receptors: which structural template to use? (2009, methodology): “The accuracy of the TM models, i.e. the structural similarity between a model and the crystallographic structure of the target was measured by RMSD, using the SUPERPOSE command of MODELLER 34 without setting a specific cutoff value.”
• Using multiple templates to improve quality of homology models in automated homology modeling (2008, methodology): “In a recent study (Wallner and Elofsson 2006), we showed that three methods, Nest (Petrey et al. 2003), Modeller (Sali and Blundell 1993), and SegMod (Levitt 1992), all perform quite well for single-template homology modeling, while several other methods frequently failed to produce…”