MMTSB toolset

MMTSB toolset integrates utilities and libraries to enhance sampling and multiscale modeling for simulations of proteins and nucleic acids.

Key Features:

• Integration with CHARMM and Amber: Interfaces with CHARMM and Amber for classical all-atom simulations.
• MONSSTER low-resolution sampling: Supports MONSSTER for lattice-based low-resolution conformational sampling.
• Multiscale model translation: Translates and integrates models between different levels of detail, including all-atom and low-resolution representations.
• Replica exchange: Implements replica exchange to enhance sampling for both all-atom and low-resolution models.
• Ensemble computing: Provides ensemble computing to apply modeling tasks across large sets of conformations using loosely coupled parallel computation on high-end parallel computers, clustered computational grids, and desktop grid environments.
• Scoring predicted conformations: Includes utilities to score predicted protein conformations to identify native-like structures.
• Ab initio peptide folding in implicit solvent: Enables ab initio folding of peptides in implicit solvent using replica exchange methods.
• Prediction of missing fragments: Supports prediction of missing fragments within larger protein structures.

Scientific Applications:

• Structure prediction and refinement: Enables protein and nucleic acid structure prediction and refinement using multiscale models and enhanced sampling.
• Extended conformational sampling: Facilitates extended conformational sampling of biomolecules using replica exchange and low-resolution sampling.
• Selection of native-like conformations: Assists in scoring and selecting predicted conformations most similar to native structures.
• Ab initio peptide folding: Applied to ab initio folding of peptides in implicit solvent.
• Predicting missing fragments: Applied to predict missing fragments within larger protein structures.

Methodology:

Implements replica exchange; lattice-based low-resolution conformational sampling via MONSSTER; interfaces with CHARMM and Amber for classical all-atom simulations; ensemble computing across large conformation sets using loosely coupled parallel computation on high-end parallel computers, clustered computational grids, and desktop grid environments; and ab initio peptide folding in implicit solvent.