ModBase

ModBase provides annotated comparative protein structure models and a repository of three-dimensional models to support structural biology and protein-structure analysis.

Key Features:

• Automated modeling (ModPipe): ModPipe performs automated comparative modeling using Modeller for fold assignment, sequence-structure alignment, model building, and model assessment.
• Model repository size: Nearly 30 million high-quality models corresponding to domains in over 4.7 million unique protein sequences.
• On-demand modeling (ModWeb): ModWeb computes or updates comparative models on demand.
• External access: Models are accessible via the Protein Model Portal.
• AllosMod Server: Models ligand-induced protein dynamics to represent conformational changes upon ligand binding.
• AllosMod-FoXS Server: Predicts structural ensembles that fit a given Small Angle X-ray Scattering (SAXS) profile.
• FoXSDock Server: Performs protein-protein docking and filters docking results based on SAXS profiles.
• SAXS Merge Server: Automates merging of SAXS profiles.
• Pose & Rank Server: Scores protein-ligand complexes for evaluation and ranking of binding interactions.

Scientific Applications:

• Structural biology: Supports protein structure prediction and analysis across diverse protein families.
• PSI:Biology initiatives: Contributed to maximizing structural coverage of the human alpha-helical transmembrane proteome.
• Virology and drug design: Supported studies determining structural determinants of specificity for HIV-1 protease.

Methodology:

ModPipe is the automated modeling pipeline; Modeller is used for fold assignment, sequence-structure alignment, model building, and model assessment. ModWeb computes or updates comparative models on demand. AllosMod models ligand-induced dynamics; AllosMod-FoXS predicts ensembles fitting SAXS profiles; FoXSDock performs docking filtered by SAXS; SAXS Merge merges SAXS profiles; Pose & Rank scores protein-ligand complexes.