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. 2004 Jan 1;32(Database issue):D217-22.
doi: 10.1093/nar/gkh095.

MODBASE, a Database of Annotated Comparative Protein Structure Models, and Associated Resources

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Free PMC article

MODBASE, a Database of Annotated Comparative Protein Structure Models, and Associated Resources

Ursula Pieper et al. Nucleic Acids Res. .
Free PMC article

Abstract

MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).

Figures

Figure 1
Figure 1
The relationships between MODBASE and associated resources. References are indicated by superscript numbers. aN. Mirkovic, M. A. Marti-Renom, A. Sali and A. N. A. Monteiro, submitted.
Figure 2
Figure 2
CHIMERA and the MultAlign Viewer extension. The barrel domains of selected enolase superfamily members are shown, with sidechains displayed for active site metal-binding residues. The multiple sequence alignment contains the corresponding sequences with the metal-binding residues colored in the same way. The CHIMERA interface allows user selections within the sequences, to highlight the corresponding regions of the structures and vice versa.
Figure 2
Figure 2
CHIMERA and the MultAlign Viewer extension. The barrel domains of selected enolase superfamily members are shown, with sidechains displayed for active site metal-binding residues. The multiple sequence alignment contains the corresponding sequences with the metal-binding residues colored in the same way. The CHIMERA interface allows user selections within the sequences, to highlight the corresponding regions of the structures and vice versa.

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