MODBASE: a database of annotated comparative protein structure models and associated resources

By Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, Mallur Srivatsan Madhusudhan, Andrea Rossi, Marc A. Martí-Renom, Rachel Karchin, Ben M. Webb, David Eramian and 4 more. 2005

705 citations recorded by the source corpus.

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 by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, ), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, ) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, ).

Subfields: Biomedical Engineering, Materials Chemistry, Molecular Biology

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Citations in the corpus

The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
Protein structure prediction from sequence variation (2012, methodology): “4 ).”
High resolution comparative modeling with RosettaCM (2013, neutral): “Fortunately, structures are now known for at least one representative of most protein families, and comparative modeling methods can be used to generate models of many proteins using these representative structures as starting points(Pieper et al., 2011).”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, methodology): “PMP relies on models provided by several research groups such as Center for Structures of Proteins in Membranes (CSMP) (12), North Eastern Structural Genomics Center (NESG) (13), New York Structural Genomics Research Consortium (NYSGRC) (14), ModBase (15), SWISS-MODEL Repository (16) and GPCRDB (17)”
Template-based protein structure modeling using the RaptorX web server (2012, background): “It has been estimated that 76% of the 4.2 million models deposited in MODBASE 21 , a database repository for theoretical structure models, are built from remote homologs.”
Progress and challenges in protein structure prediction. (2008, methodology): “Based on about 40 000 structures in the PDB library (many are redundant) [3], 4 million models/fold-assignments can be obtained by a simple combination of the PSI-BLAST search and the comparative modeling technique [4 ].”
Structural genomics is the largest contributor of novel structural leverage (2009, background): “Our restriction to E-values B 10 implies that the inferred structural models are of relatively high reliability and cover most of the aligned regions [16, 25]; higher leverage and coverage can be achieved at the expense of accuracy [3, 17, 27, 33].”
Statistical potential for assessment and prediction of protein structures (2006, methodology): “The moulder decoy set is derived by iterative target-template alignment and comparative model building of 20 target sequences Bowie, Brooks target, based on a wide range of target-template alignment accuracy.”
The Protein Model Portal (2008, methodology): “The protein modeling portal federates protein model data from different providers (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, Mod-Base [10], and SWISS-MODEL Repository [22, 23]) by integrating model meta information: the segment of a target protein for which a model is available, template structure…”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “Searching for existing models in the ModBase database ModBase (http://salilab.org/modbase/; Pieper et al., 2014) is our database of annotated comparative protein structure models.”
The Protein Structure Initiative: achievements and visions for the future (2012, background): “These structures are being used as templates for modelling tens of thousands of homologous proteins [12-17] and provide a database of protein sequences, structures, and biophysical properties (e.g. chemical shifts) that also inform the fields of protein structure prediction, design, and engineering.”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, neutral): “…(Roche et al., 2011) I-Tasser http://zhanglab.ccmb.med.umich.edu/I-TASSER/ (Zhang, 2013) ModBase http://salilab.org/modbase/ (Pieper et al., 2011) Modeller/ModWeb http://salilab.org/modeller/ (Pieper et al., 2011; Yang et al., 2012) Pcons.net http://pcons.net/ (Larsson et…”
How well can the accuracy of comparative protein structure models be predicted? (2008, background): “As a result, the utility of comparative modeling is significantly reduced, because 76% of all comparative models are based on less than 30% sequence identity (Pieper et al. 2006).”
Gene3D: expanding the utility of domain assignments (2015, background): “7 or a normalized DOPE score <0 (as described in (19)).”
FreeContact: fast and free software for protein contact prediction from residue co-evolution (2014, background): “Homology modeling [4] or comparative modeling [5] is the only bridge that allows reliable modeling of 3D structure for about 20-40% of the residues in all known proteins [6].”
Ab initio protein structure prediction using chunk-TASSER. (2007, background): “E () { 0 r> = ro, (3) rep r = (ro-r)'/r r<ro, ,”