Comparative Protein Structure Modeling of Genes and Genomes
Top Cited Papers
- 1 June 2000
- journal article
- research article
- Published by Annual Reviews in Annual Review of Biophysics and Biophysical Chemistry
- Vol. 29 (1), 291-325
- https://doi.org/10.1146/annurev.biophys.29.1.291
Abstract
▪ Abstract Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target–template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence–structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely 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.Keywords
This publication has 99 references indexed in Scilit:
- Homology-based fold predictions for Mycoplasma genitalium proteinsJournal of Molecular Biology, 1998
- Who checks the checkers? four validation tools applied to eight atomic resolution structuresJournal of Molecular Biology, 1998
- AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMRJournal of Biomolecular NMR, 1996
- Structural Features can be Unconserved in Proteins with Similar Folds: An Analysis of Side-chain to Side-chain Contacts Secondary Structure and AccessibilityJournal of Molecular Biology, 1994
- Comparative Protein Modelling by Satisfaction of Spatial RestraintsJournal of Molecular Biology, 1993
- Prediction of Protein Secondary Structure at Better than 70% AccuracyJournal of Molecular Biology, 1993
- Protein folding: Effect of packing density on chain conformationJournal of Molecular Biology, 1991
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990
- Canonical structures for the hypervariable regions of immunoglobulinsJournal of Molecular Biology, 1987
- CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsJournal of Computational Chemistry, 1983