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Comparative protein modelling by satisfaction of spatial restraints.
A comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures, which is automated and illustrated by the modelling of trypsin from two other serine proteinases.
Comparative Protein Structure Modeling Using MODELLER
This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing
A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.
Comparative protein structure modeling of genes and genomes.
- M. Martí-Renom, A. C. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali
- BiologyAnnual review of biophysics and biomolecular…
- 6 August 2002
There is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes and to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.
Protein structure modeling with MODELLER.
This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure, and shows the potential for this technique to bridge the sequence-structure gap in protein structure modeling.
Comparative Protein Structure Modeling Using Modeller
This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Statistical potential for assessment and prediction of protein structures
To facilitate its use in various applications, such as model assessment, loop modeling, and fitting into cryo‐electron microscopy mass density maps combined with comparative protein structure modeling, DOPE was incorporated into the modeling package MODELLER‐8.
Modeller: generation and refinement of homology-based protein structure models.
Modeling of loops in protein structures
A new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment is described.
Evaluation of comparative protein modeling by MODELLER
- A. Sali, Liz Potterton, F. Yuan, H. V. van Vlijmen, M. Karplus
- Biology, ChemistryProteins
- 1 November 1995
We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for…