338 Database entries


Ratings:    0  votes
Please vote:   

OS: Linux, Windows, ...

ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.

ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies.

Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed.

Ten reasons to try ZMM

1. ZMM is universal: you can model drugs, peptides, proteins, nucleic acid, and ligand-receptor complexes
2. ZMM is fast. It minimizes energy in the space of generalized coordinates (Zhorov, 1981; Zhorov, 1982) and employs highly efficient method of Monte Carlo minimization (Li and Scheraga, 1987)
3. ZMM is flexible: large number of controls can tune ZMM for a specific task
4. ZMM is user-friendly. It includes a graphic interface MVM and can also be used with any molecular graphics program, e.g. RASMOL and PYMOL
5. ZMM is easy to use: you can import molecular structure from a PDB file in one command or mutate a protein in one keystroke
6. ZMM is easy to learn. It includes comprehensive description and hundreds of examples
7. ZMM integrates 30+ years of experience in molecular modeling of biomolecular systems
8. 200+ publications on ZMM-based studies are available
9. ZMM runs under Windows, UNIX, and Linux
10. Parallel ZMM for UNIX and Linux is available

Link: http://www.zmmsoft.com/