ModBase, a database of annotated comparative protein structure models and associated resources
By Ursula Pieper, Ben M. Webb, G. Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, M. Hammel and 3 more. Nucleic Acids Res., 2013
416 citations recorded by the source corpus.
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/modweb). ModBase models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/d41cd44856f7a9bed1058223e64a9142d79b8d54
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Andrej Sali
- Torsten Schwede
- Ben M. Webb
- Yang Zhang
- Andriy Kryshtafovych
- Krzysztof Fidelis
- Roland L. Dunbrack
- John Moult
In Molecular Biology
- Torsten Schwede
- Andrej Sali
- Yang Zhang
- Ben M. Webb
- Andriy Kryshtafovych
- Krzysztof Fidelis
- David Baker
- Roland L. Dunbrack
Citations in the corpus
- RCSB Protein Data Bank: Enabling biomedical research and drug discovery (2019, methodology): “Protein Feature View offers graphical summaries of full-length UniProt 16 protein sequences and how they correspond to PDB entries, together with annotations from external databases (such as Pfam), 17 homology model information, 18,19 predicted regions of protein disorder, and hydrophobic regions.”
- The functional landscape of the human phosphoproteome (2019, neutral): “0 (Pieper et al. 2014).”
- Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, methodology): “The Protein Model Portal in particular provides access to models calculated by SWISS-MODEL (Kopp and Schwede, 2004), ModBase (Pieper et al., 2006), as well as models produced by the four PSI large-scale production centers (http://www.”
- In silico methods and tools for drug discovery (2021, methodology): “Diverse tools and online resources for homology modeling are available; these tools include MODELER [136], SwissModel [137], Mod web [138], and Phyre2 [139].”