Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
By Donald Petrey, Zhexin Xiang, Christopher Tang, Lei Xie, Marina Gimpelev, T. Mitros, C. Soto, Sharon Goldsmith-Fischman, A. Kernytsky, Avner Schlessinger and 3 more. Proteins: Structure, Function, and Bioinformatics, 2003
313 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3776f4f4514d75fd941c63e21b80d39ea5777fa1
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In Materials Chemistry
- Liam J. McGuffin
- Arne Elofsson
- Björn Wallner
- Yang Zhang
- David T. Jones
- András Szilágyi
- Petras J. Kundrotas
- Johannes Söding
In Molecular Biology
- Yang Zhang
- Liam J. McGuffin
- Arne Elofsson
- Björn Wallner
- David T. Jones
- Torsten Schwede
- Jianlin Cheng
- Jinbo Xu
Citations in the corpus
- Templates are available to model nearly all complexes of structurally characterized proteins (2012, methodology): “The protein models were built by the NEST program from the JACKAL package (20) with the default parameters.”
- Using multiple templates to improve quality of homology models in automated homology modeling (2008, background): “It was one of the first fully automated programs and it is also relatively fast, making it suitable, e.g., for whole-genome modeling (Marti-Renom et al. 2000; Pieper et al. 2004).”
- Template-based structure modeling of protein-protein interactions (2013, methodology): “In several methods such as HOMCOS [45,49] and Interactome3D [65 ], and HOMBACOP [25], the monomerbased comparative modeling programs MODELLER [66] and NEST [67] are used to build complete complex models.”
- Ab initio modeling of small proteins by iterative TASSER simulations (2007, unknown): “We also tried MODELLER [3] and NEST [44] softwares to refine the centroid models.”
- MEDELLER: homology-based coordinate generation for membrane proteins (2010, background): “Membrane proteins (MP) constitute about 30% of all known proteins and are one of the largest classes of drug targets.”
- Natively Unstructured Loops Differ from Other Loops (2007, unknown): “Visualization was done using GRASP2 [85].”
- Improving sequence-based fold recognition by using 3D model quality assessment (2005, methodology): “CTrip (Petrey et al ., 2003) was used from the Jackal protein structure modeling package (http://honiglab.cpmc.columbia.edu/programs/jackal/index.html) in order to generate the backbone atoms for each of the models.”
- Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling (2015, methodology): “NEST [11] implements an artificial evolution algorithm where changes from the template structure such as substitutions, insertions and deletions are made one at a time, and each mutation is followed by an energy minimization.”