Protein Structure Modeling with MODELLER
Top Cited Papers
- 1 January 2008
- book chapter
- Published by Springer Nature
- Vol. 426, 145-159
- https://doi.org/10.1007/978-1-60327-058-8_8
Abstract
Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protcols has resulted in models of useful accuracy for domains in more than half of all known protein sequences.Keywords
This publication has 39 references indexed in Scilit:
- Statistical potential for assessment and prediction of protein structuresProtein Science, 2006
- A composite score for predicting errors in protein structure modelsProtein Science, 2006
- A supersecondary structure library and search algorithm for modeling loops in protein structuresNucleic Acids Research, 2006
- Variable gap penalty for protein sequence–structure alignmentProtein Engineering, Design and Selection, 2006
- Statistical potentials for fold assessmentProtein Science, 2002
- Modeling of loops in protein structuresProtein Science, 2000
- All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of ProteinsThe Journal of Physical Chemistry B, 1998
- Empirical statistical estimates for sequence similarity searchesJournal of Molecular Biology, 1998
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Comparative Protein Modelling by Satisfaction of Spatial RestraintsJournal of Molecular Biology, 1993