Modeling of loops in protein structures
By András Fiser, Richard K. G. Do, Andrej Sali. 2000
2,117 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
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In Materials Chemistry
In Molecular Biology
Citations in the corpus
- Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome (2010, methodology): “Models resulting from FFAS (34) hits to 2g0u chain A and 2jow were refined using Modeler (35), resulting in confident structure predictions for residues 23–98of PrgJ.”
- GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors (2016, methodology): “An optional stage can follow where selected loop regions are remodeled using the LoopModel (29) algorithm from Modeller.”
- Statistical potentials for fold assessment (2002, neutral): “The Ramachandran maps were extracted from a representative set of 1000 protein structures (217,807 residues) that shared <60% sequence identity to each other or had >30-residue length difference, and were determined by X-ray crystallography at a resolution of 2.3 Å or better (Fiser et al. 2000).”
- Cyclic coordinate descent: A robotics algorithm for protein loop closure (2003, methodology): “Most loop methods have not been tested in true homology modeling situations, but rather in the more artificial situation of replacing a loop back into its own native structure Both Modeller (Fiser et al. 2000) and the “scaling relax-ation” method of Zheng et al. (1992) build initial conformations th”
- Statistical potential for assessment and prediction of protein structures (2006, methodology): “The 4state-reduced decoy set, from 632 to 689 models per target (seven targets in generated using a four-state off-lattice model with relaxation method (Park and Levitt 1996). annealing protocol (Simons et al. 1997, 1999).”
- SsNAC23, a member of the NAC domain protein family, is associated with cold, herbivory and water stress in sugarcane (2005, methodology): “The quality of the predicted fold was evaluated in MODELLER using the score of the variable target function method [36].”
- Tools for comparative protein structure modeling and analysis (2003, methodology): “Apart from model building, MODELLER can perform additional auxiliary tasks, including alignment of two protein sequences or their profiles, multiple alignment of protein sequences and/or structures, calculation of phylogenetic trees and de novo modeling of loops in protein structures (18).”
- Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “The method was tested on a large number of loops of known structure, both in native and near-native environments (Fiser et al., 2000).”
- Protein-protein docking with backbone flexibility. (2007, positive): “The monomeric protein test set for loop modeling was originally compiled by Fiser et al.(44) It contains 40 proteins for each of the 8- and 12-residue loop subsets.”
- How well can the accuracy of comparative protein structure models be predicted? (2008, background): “Predicting the absolute accuracy of a model is particularly difficult due to the lack of principled reasons why an individual assessment score should correlate well with accuracy measures such as RMSD, particularly if the models are not native-like (Fiser et al. 2000).”
- Scoring function for automated assessment of protein structure template quality (2004, methodology): “The TM-score, as well as the Maxsub and GDT_TS scores, of the initial templates are evaluated on the basis of their correlations to the quality of the final full-length models in the benchmark targets built by the widely-used protein modeling software MODELLER.(7,10)”