ALMOST

ALMOST performs structure determination and analysis of proteins and nucleic acids by integrating experimental measurements as conformational restraints and analyzing structural and dynamical properties.

Key Features:

• Structure Determination: Integrates experimental measurements as conformational restraints, including distance restraints from nuclear Overhauser effect (NOE) measurements, orientational restraints from residual dipolar couplings (RDCs), and structural restraints informed by chemical shifts.
• Molecular Analysis: Implements algorithms for comprehensive analysis of structural and dynamical features of proteins and nucleic acids, including assessment of conformational flexibility and stability.
• Molecular Simulations and Design: Supports a range of molecular modeling and simulation approaches, including homology modeling, de novo design, and ab-initio calculations.
• All-atom Simulation: Operates as an all-atom molecular simulation toolkit for detailed structural and dynamical studies.

Scientific Applications:

• Structural Biology: Determination of protein and nucleic acid structures using NOE, RDCs, and chemical shift restraints.
• Molecular Dynamics and Conformational Analysis: Analysis of biomolecular dynamics, conformational flexibility, and stability.
• Computational Design and Modeling: Homology modeling, de novo design, and ab-initio modeling for structure prediction and design.
• Drug Design and Protein Folding Studies: Application to drug design efforts and studies of protein folding and function.

Methodology:

Integrates experimental restraints (NOE distance restraints, RDC orientational restraints, chemical shift–derived restraints), applies algorithms for structural and dynamical analysis, and implements homology modeling, de novo design, and ab-initio calculation methods.