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Protocols

moloc specifications

Information


Unique identifier OMICS_28052
Name moloc
Alternative name multiple-trait-coloc
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Panos Roussos
  • person_outline Claudia Giambartolomei

Publication for multiple-trait-coloc

moloc citations

 (27)
library_books

Discovery of the first dual GSK3β inhibitor/Nrf2 inducer. A new multitarget therapeutic strategy for Alzheimer’s disease

2017
Sci Rep
PMCID: 5374710
PMID: 28361919
DOI: 10.1038/srep45701

[…] and compared with the score algorithm, protein interaction, hydrogen bonding, and affinity interaction energies and ordered by the energy of interaction protein-ligand. Complexes were optimized using Moloc software (www.moloc.ch) with standard force field and optimization parameters. During energy minimization the position of amino acid side chains were fixed while allowing all ligand atoms to mov […]

library_books

FACT is a sensor of DNA torsional stress in eukaryotic cells

2017
Nucleic Acids Res
PMCID: 5389579
PMID: 28082391
DOI: 10.1093/nar/gkw1366

[…] A superimposition of 3D conformer of CBL0137 with DNA was analyzed by computer modelling. The molecule docking to DNA was performed with the MOLOC (Gerber Molecular Design) molecular mechanics tools and by GOLD software (Cambridge Crystallographic Data Center). […]

library_books

Determinants of FIV and HIV Vif sensitivity of feline APOBEC3 restriction factors

2016
Retrovirology
PMCID: 4930625
PMID: 27368163
DOI: 10.1186/s12977-016-0274-9

[…] . The linker domain was manually positioned near the linker region gap, unstructured parts were connected to the rest of the feline A3Z2Z3 and minimized using the MAB force field [] as implemented in Moloc, thereby keeping all other protein atoms fixed. […]

library_books

Chalcone based Selective Inhibitors of a C4 Plant Key Enzyme as Novel Potential Herbicides

2016
Sci Rep
PMCID: 4893628
PMID: 27263468
DOI: 10.1038/srep27333

[…] The MAB force field as implemented in the program Moloc was used to minimize the docking poses in the binding pocket. For this, the protein atoms were defined as stationary, and only the ligand was allowed to move. […]

library_books

Uncoupling JAK2 V617F activation from cytokine induced signalling by modulation of JH2 αC helix

2016
PMCID: 4888464
PMID: 27029346
DOI: 10.1042/BCJ20160085

[…] and a partial model of the wild-type JAK2 JH2 domain (PDB: 4FVP with residues 586–600 and 617 deleted). Refinement was performed using PHENIX [] interspersed with iterative cycles of rebuilding using Moloc []. […]

library_books

Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance

2016
PLoS One
PMCID: 4773095
PMID: 26930060
DOI: 10.1371/journal.pone.0149903

[…] g backbone torsion angles in the region immediately C-terminal to helix α4. Afterwards, helix α4 and the adjacent loops were energy minimized with the MAB force field [] as implemented in the program Moloc; all other atoms of NsrR-RD were kept fixed. The result is highlighted in . The energy minimized structure of NsrR-RD was then superimposed on the dimeric structure of KdpE [].The putative funct […]

Citations

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moloc institution(s)
Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, CA, USA; New York Genome Center, New York, NY, USA; Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Lundbeck Foundation Initiative of Integrative Psychiatric Research (iPSYCH), Aarhus University, Aarhus, Denmark; Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA; Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA; Departments of Mental Health and Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
moloc funding source(s)
Supported in part by the National Institutes of Health (R01AG050986 Roussos and R01MH109677), Brain Behavior Research Foundation (20540), Alzheimer's Association (NIRG340998) the Veterans Affairs (Merit grant BX002395).

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