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MM-ISMSA specifications


Unique identifier OMICS_08210
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained No


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MM-ISMSA citations


High affinity ligands of the colchicine domain in tubulin based on a structure guided design

Sci Rep
PMCID: 5844890
PMID: 29523799
DOI: 10.1038/s41598-018-22382-x

[…] r the temperature and pressure baths were 1.0 and 0.2 ps, respectively. 500 sets of coordinates from the resulting MD trajectory were analyzed by means of the cpptraj module in AMBER and our in-house MM-ISMSA program. […]


WW Domains of the Yes Kinase Associated Protein (YAP) Transcriptional Regulator Behave as Independent Units with Different Binding Preferences for PPxY Motif Containing Ligands

PLoS One
PMCID: 4301871
PMID: 25607641
DOI: 10.1371/journal.pone.0113828

[…] cycle in vacuum using the AMBER ff10 force field []. The quality of the models was evaluated using PROCHECK []. The hydrogen bond interactions in the protein-ligand interfaces were evaluated with the MM-ISMSA software [] considering that the distance between the hydrogen and acceptor atoms is within 1.5 Å and 2.4 Å, the angle between donor, hydrogen, and acceptor atoms varies within 130º and 165º; […]


Esterase LpEst1 from Lactobacillus plantarum: A Novel and Atypical Member of the αβ Hydrolase Superfamily of Enzymes

PLoS One
PMCID: 3963902
PMID: 24663330
DOI: 10.1371/journal.pone.0092257

[…] warded the best score according to the CRScore function.The nature of the interactions and the residues involved in dimerization of LpEst1 and its bacterial HSL homologs were analyzed by means of the MM-ISMSA method , which includes the non-bonding term of the AMBER99sb force field and a desolvation term as calculated by the Implicit Solvation Method (ISM) . The per-residue energy decomposition p […]

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MM-ISMSA institution(s)
Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco UAM, Madrid, Spain

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