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ConfGen specifications

Information


Unique identifier OMICS_18794
Name ConfGen
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline John Shelley <>

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Publication for ConfGen

ConfGen in publications

 (26)
PMCID: 5817085
PMID: 29492402
DOI: 10.3389/fchem.2018.00023

[…] generation of stereoisomers, neutralizing the charges on the structures and generating ionization states at ph 7.0 using opls2005 force fields. one thousand conformers were generated per compound by confgen module of schrodinger suite software (watts et al., ). all the conformations were pre-minimized and post-minimized. opls2005 force field was used with gb/sa water solvent treatment […]

PMCID: 5806266
PMID: 29456971
DOI: 10.1186/s40709-018-0074-6

[…] module. the molecular structure of the butyl-butyrate was built and prepared using the build and the ligprep module, respectively. different conformations were generated with the advanced search of confgen module, by selecting water as solvent and the truncated newton (tcng) method for minimization (100 iterations). a 30 × 30 × 30 å3 grid box with 10 × 10 × 10 å3 default inner box was centered […]

PMCID: 5735092
PMID: 29255256
DOI: 10.1038/s41598-017-17672-9

[…] code), the proposed consensus core sequence of impα/β1 recognised nlss– served as the basis for selecting the ‘core’ of the c nls (amino acids #6–11) (table , fig. ); conformers were generated using confgen (schrodinger, portland, or, usa) and then docked using glide (schrodinger, portland, or, usa) to estimate the free energy of binding in the impα binding pocket. notably, the best glide […]

PMCID: 5346735
PMID: 27791197
DOI: 10.18632/oncotarget.12836

[…] glide [] [] [] was also used for docking experiments to assess the possible binding mode between egcg and the n-terminal domain of traf6. in order to enhance the conformational sampling, we used the confgen module [] in the schrödinger software package to generate 254 conformations of the egcg for protein-ligand docking. the binding pose with the lowest xp gscore (−7.952 kcal/mol) was considered […]

PMCID: 4932017
PMID: 27429875
DOI: 10.1186/s40064-016-2589-3

[…] of finding geometry close to the putative binding mode. phase provides two built-in approaches, both of which employ the macromodel conformational search engine. conformers were generated using confgen (watts et al. ) followed by minimization of each generated structure using merck molecular force field (mmff)., the chemical features or the pharmacophore sites for the molecules were defined […]


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ConfGen institution(s)
Schrodinger, LLC, Portland, OR, USA; Schrodinger, LLC, New York, NY, USA; D. E. Shaw India Software Private Limited, Sanali Infopark, Banjara Hills, Hyderabad, Andhra Pradesh, India; Department of Chemistry, Columbia University, Broadway, New York, NY, USA

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