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Pmx specifications


Unique identifier OMICS_17115
Name Pmx
Alternative name pymacs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Numpy, Scipy, Matplotlib
Maintained Yes




No version available


  • person_outline Vytautas Gapsys

Publication for Pmx

Pmx citations


Computational Analysis of the Molecular Mechanism of RamR Mutations Contributing to Antimicrobial Resistance in Salmonella enterica

Sci Rep
PMCID: 5645378
PMID: 29042652
DOI: 10.1038/s41598-017-14008-5

[…] The pmx tool was used to construct the hybrid topologies of the system used in the free energy calculations,. This tool automatically generates hybrid structures and topologies for amino acid mutations th […]


Zinc binding to RNA recognition motif of TDP 43 induces the formation of amyloid like aggregates

Sci Rep
PMCID: 5533730
PMID: 28754988
DOI: 10.1038/s41598-017-07215-7

[…] Coordinates for RNA-TDP43 complex NMR derived structure (PDBID: 4BS2) was obtained from the PDB data bank. The python PMX module was used to parse the atom coordinates. For atoms ND1, NE2 and SG in HIS and CYS residues neighboring atoms with names ND1, NE2, SG, OE1 and OD1 were searched with distances less than 6 Å. […]


Synthesis and crystal structure of [2,7,12 trimethyl 3,7,11,17 tetra­aza­bicyclo­[11.3.1]hepta­deca 1(17),13,15 triene κ4 N]copper(II) bis­(perchlorate)

PMCID: 4992927
PMID: 27555952
DOI: 10.1107/S2056989016009701

[…] (3-amino­prop­yl)amine. Their pioneering work enabled subsequent syntheses of various pyridine-containing macrocycles (Rezaeivala & Keypour, 2014), including a family of complexes with appended arms (PyMACs) (Organo et al., 2009; Herrera et al., 2003) as shown in Fig. 1.Various metal ions have been incorporated into PyMAC ligands, and the resulting complexes often showed inter­esting catalytic pro […]


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Pmx institution(s)
Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany

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