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Protocols

MacroModel specifications

Information


Unique identifier OMICS_18800
Name MacroModel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline QikProp Team

Additional information


A registration is needed to access to tool. Tuto: https://www.schrodinger.com/training/macromodel-workshop-tutorial

MacroModel citations

 (19)
call_split

Lactones from the Sponge Derived Fungus Talaromyces rugulosus

2017
Mar Drugs
PMCID: 5706048
PMID: 29135916
DOI: 10.3390/md15110359
call_split See protocol

[…] -height width (corresponding to c.a. 14 and 17 nm at 240 nm), using dipole-velocity computed rotational strengths []. Mixed torsional/low mode conformational searches were carried out by means of the Macromodel 10.8.011 software (New York, NY, USA) using Merck Molecular Force Field (MMFF) with implicit solvent model for CHCl3 applying a 21 kJ/mol energy window []. Boltzmann distributions were esti […]

call_split

Structure Guided Design of C4 alkyl 1,4 dihydro 2H pyrimido[4,5 d][1,3]oxazin 2 ones as Potent and Mutant Selective Epidermal Growth Factor Receptor (EGFR) L858R/T790M Inhibitors

2017
Sci Rep
PMCID: 5476563
PMID: 28630494
DOI: 10.1038/s41598-017-04184-9
call_split See protocol

[…] group was formed by the build panel in Maestro; Finally, to fix the bond lengths and eliminate steric clashed, the covalently modified inhibitor-kinase complexes were minimized in water solvent using MacroModel application with flexible ligand and constrained protein.The scaffold hopping was conducted by SHAFTS, . The query molecule is the docked pose of compound 9 obtained from the above docking […]

library_books

Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network

2017
Sci Rep
PMCID: 5364480
PMID: 28337996
DOI: 10.1038/srep44948

[…] NYGAPEPNVPS and NYGAQETNVSS peotides were investigated for their conformational behavior in solution using the MacroModel software. The two peptides were sketched using the Maestro interface, capped with ACE and NMA residues, and were submitted to 500000 steps of mixed torsional/large-scale low mode sampling c […]

library_books

A compound based proteomic approach discloses 15 ketoatractyligenin methyl ester as a new PPARγ partial agonist with anti proliferative ability

2017
Sci Rep
PMCID: 5259791
PMID: 28117438
DOI: 10.1038/srep41273

[…] pound 1 was retrieved from the Cambridge Structural Database (refcode: YALXIU) and modified with the fragment dictionary of Maestro. The ligand was then preprocessed with LigPrep 3.3 and optimized by Macromodel 10.7, using the MMFFs force field with the steepest descent (1000 steps) followed by truncated Newton conjugate gradient (500 steps) methods. Partial atomic charges were computed using the […]

library_books

Merosesquiterpene Congeners from the Australian Sponge Hyrtios digitatus as Potential Drug Leads for Atherosclerosis Disease

2016
Mar Drugs
PMCID: 5295226
PMID: 28036007
DOI: 10.3390/md15010006

[…] studies as 5S,8S,10S []. To confirm that 1 and 2 possess the same absolute configuration, ECD experimental and calculation studies by quantum mechanics were carried out. The OPLS-2005 force field in MacroModel was used to perform a conformational search with relative energies within 21 kJ/mol [] and the basic set level (b3lyp/631gd) in solvent phase using the Gaussian 09 program, which was chosen […]

library_books

High Resolution Genetics Identifies the Lipid Transfer Protein Sec14p as Target for Antifungal Ergolines

2016
PLoS Genet
PMCID: 5147771
PMID: 27855158
DOI: 10.1371/journal.pgen.1006374

[…] used as a starting point for the docking. The docking procedure was carried out using Glide SP within the Maestro Schrödinger Suite. After docking the complex protein-ligand has been minimized using MacroModel within the Maestro Schrödinger Suite, allowing the ligand to be flexible and keeping the protein rigid. […]


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