tnm

The program tnm computes the normal modes of protein structure <pdb1> in the space of torsion angles and other relevant internal coordinates such as inter-chain rigid body degrees of freedom and pseudo-bonds between protein regions separated by disordered loops. These normal modes allow computing the statistical physics of the native state of the protein within the harmonic approximation. The program can perform several computational analysis of atomic fluctuations, functional sites and conformational changes.

Info

Members (researchers): Ugo Bastolla

Research Groups: Computational biology and Bioinformatics (CBM): from Proteins to Ecosystems

Contact Email: ubastolla@cbm.csic.es

Tool Repository: https://github.com/ugobas/tnm

Documentation: https://github.com/ugobas/tnm

Publications DOI: doi:10.1103/PhysRevLett.104.228103

Institution: Centro de Biología Molecular Severo Ochoa (CBM)

Application domain:

Biomolecular simulation, Biosystems Modeling, Computational models and simulations, Molecular flexibility, Mutation Analysis and design, Structural bioinformatics, Structure-function relationship

Technical details
Type of application
  • C package for compiling the executable program
Software compatibility
  • Linux
Hardware requirements
  • Any linux computer
Programming language
  • C
Type of containerization
  • None
Wrapper type
  • None
Input file formats
  • pdb
Output file formats
  • Other
  • pdb
Compatibility with other tools
  • My own program SSCPE for comuting structure-constrained substitution processes for phylogenetic inference