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Protocols

MOLMOL specifications

Information


Unique identifier OMICS_19957
Name MOLMOL
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Reto Koradi

Additional information


http://www.csb.yale.edu/userguides/graphics/molmol/html/ http://www.csb.yale.edu/userguides/graphics/molmol/tutorial/

Publication for MOLMOL

MOLMOL citations

 (364)
library_books

In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design

2018
Nat Commun
PMCID: 5902452
PMID: 29662055
DOI: 10.1038/s41467-018-03746-3

[…] d and additional allowed regions. ProSA indicates the fold quality by means of the Z-score. The display, analysis, and manipulation of the three-dimensional structures were performed with the program MOLMOL and PyMOL (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC). […]

call_split

LyeTxI b, a Synthetic Peptide Derived From Lycosa erythrognatha Spider Venom, Shows Potent Antibiotic Activity in Vitro and in Vivo

2018
Front Microbiol
PMCID: 5897548
PMID: 29681894
DOI: 10.3389/fmicb.2018.00667
call_split See protocol

[…] The stereochemical quality of the lowest energy structures was analyzed by PROCHECK-NMR (). The display, analysis, and manipulation of the three-dimensional structures were performed with the program MOLMOL (). […]

library_books

Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB

2018
PMCID: 5890618
PMID: 29526435
DOI: 10.1016/j.str.2018.02.007

[…] wenty structures with the lowest energy values were selected out of 200 and subjected to a water refinement process. The final ensemble of the structure (PDB: 5N7Y) was analyzed and represented using MOLMOL () and PyMOL. […]

library_books

Competition between Li+ and Na+ in sodium transporters and receptors: Which Na+ Binding sites are “therapeutic” Li+ targets?† †Electronic supplementary information (ESI) available: Table S1 listing all PDB entries of transporter and receptor structures with Na+ bound in the allosteric sites. Table S2 listing the relative % SASA and hydrogen bonds for the Na+ coordinating residues in the representative PDB structures. See DOI: 10.1039/c7sc05284g

2018
PMCID: 5944251
PMID: 29780538
DOI: 10.1039/c7sc05284g

[…] or a given structure, we computed the % ratio of the solvent-accessible surface area (SASA) of the residue X in the protein to the accessible surface area of X in the tripeptide –Gly–X–Gly– using the MOLMOL program with a solvent probe radius of 1.4 Å. For a given structure, we also computed all hydrogen bonds made by the Na+-ligating residues using the HBPLUS Hydrogen Bond Calculator version 3.15 […]

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Peptide ion channel toxins from the bootlace worm, the longest animal on Earth

2018
Sci Rep
PMCID: 5864730
PMID: 29567943
DOI: 10.1038/s41598-018-22305-w
call_split See protocol

[…] he 20 models with best stereochemistry chosen to represent the solution structure of α-1. PDB ID: 6ENA. Atomic RMSD was calculated over the residues between the first and last cysteine residues using MOLMOL, Table . The Dali server was used to identify structural homologues, regardless of sequence similarity, Fig. . […]

library_books

Solution structure of extracellular loop of human β4 subunit of BK channel and its biological implication on ChTX sensitivity

2018
Sci Rep
PMCID: 5854672
PMID: 29545539
DOI: 10.1038/s41598-018-23016-y

[…] 3°. The entire structure statistics for them were evaluated with PROCHECK and PROCHECK-NMR and summarized in Table . All of the structure figures were generated using the PyMOL (http://pymol.org/) or MOLMOL programs. The structural analysis was displayed in Fig. . […]


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MOLMOL institution(s)
lnstitut fiir Molekularbiologie und Biophysik, EidgenOssische Teehnische Hochschule-HOnggerberg, Zurich, Switzerland
MOLMOL funding source(s)
Supported by BRUKER/Spectrospin.

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