Tools for comparative protein structure modeling and analysis

@article{Eswar2003ToolsFC,
  title={Tools for comparative protein structure modeling and analysis},
  author={Narayanan Eswar and Bino John and Nebojsa Mirkovic and Andr{\'a}s Fiser and Valentin A. Ilyin and Ursula Pieper and Ashley C. Stuart and Marc A. Mart{\'i}-Renom and Mallur S. Madhusudhan and Bozidar Yerkovich and Andrej Sali},
  journal={Nucleic acids research},
  year={2003},
  volume={31 13},
  pages={
          3375-80
        }
}
The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a… 

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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.
Comparative Protein Structure Modeling Using MODELLER
TLDR
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.
MODBASE: a database of annotated comparative protein structure models and associated resources
MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated
modbase, a database of annotated comparative protein structure models and associated resources
TLDR
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models that calculates comparative models on demand, through an interface to the MODWEB modeling server.
ModBase, a database of annotated comparative protein structure models and associated resources
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Comparative Protein Structure Modeling Using Modeller
TLDR
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.
Comparative Protein Structure Modeling Using MODELLER
TLDR
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.
Comparative Protein Structure Modeling Using MODELLER
TLDR
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.
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References

SHOWING 1-10 OF 35 REFERENCES
MODBASE, a database of annotated comparative protein structure models
TLDR
MODBASE is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER.
Comparative protein structure modeling of genes and genomes.
TLDR
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.
Derivation of rules for comparative protein modeling from a database of protein structure alignments
TLDR
A database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling are described, including the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues.
EVA: evaluation of protein structure prediction servers
TLDR
EVA (http://cubic.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods, and provides useful information to developers as well as users of prediction methods.
Protein Structure Prediction and Structural Genomics
TLDR
This Viewpoint begins by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes.
EVA: continuous automatic evaluation of protein structure prediction servers
TLDR
EVA is described, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion, that evaluates the performance of a variety of prediction methods available through the internet.
Comparative protein modelling by satisfaction of spatial restraints.
TLDR
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.
DBAli: a database of protein structure alignments
TLDR
The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP and CE, which allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence-sequence and sequence-structure alignment methods under a variety of conditions.
ModView, visualization of multiple protein sequences and structures
TLDR
ModView integrates a multiple structure viewer, a multiple sequence alignment editor, and a database querying engine that makes it useful for teaching and presentations and suitable as a graphical interface to various databases.
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.
  • R. Sánchez, A. Sali
  • Biology, Engineering
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
The fold assignment, comparative protein structure modeling, and model evaluation were automated completely and resulted in all-atom 3D models for substantial segments of 1,071 of the yeast proteins, only 40 of which have had their 3D structure determined experimentally.
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