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.
Basic Information
| Repository | https://github.com/ugobas/tnm |
| Documentation | https://github.com/ugobas/tnm |
| Seminar | Ugo Bastolla presents the tools TNM, PC_ali & SSCPE |
| Main publication (DOI) | 10.1103/PhysRevLett.104.228103 view |
| Contact email | ubastolla@cbm.csic.es |
| Authors/Maintainers | Ugo Bastolla |
| Type of application | Package for compiling the executable program |
| Programming languages | C |
| Keywords | Computational Methods, Structural bioinformatics, Molecular flexibility, Computational models and simulations, Biosystems Modeling, Mutation Analysis and design, Biomolecular simulation, Structure-function relationship |
Technical details
| Input file formats | pdb |
| Output file formats | pdb, Other |
| Software compatibility | Linux |
| Hardware requirements | Any linux computer |
| Type of containerization | None |
| Wrapper type | None |
| Compatible tools | My own program SSCPE for comuting structure-constrained substitution processes for phylogenetic inference |
| Funding resource | National competitive funding |
| Funding support | No funding |
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| Citations (last 12 months) | <100 (~2 as of 15/10/2026) |
| Citations (since first release) | <100 (81 as of 15/10/2026) |
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