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Number of citations per year for the bioinformatics software tool BioLuminate
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Protocols

BioLuminate specifications

Information


Unique identifier OMICS_18933
Name BioLuminate
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Free trial Yes
Registration required Yes
Maintained Yes

Subtool


  • AggScore

Versioning


No version available

Documentation


Maintainer


  • person_outline QikProp Team

Additional information


.

Publications for BioLuminate

BioLuminate citations

 (16)
library_books

Structural Insight Into the Role of Mutual Polymorphism and Conservatism in the Contact Zone of the NFR5–K1 Heterodimer With the Nod Factor

2018
Front Plant Sci
PMCID: 5909492
PMID: 29706972
DOI: 10.3389/fpls.2018.00344

[…] We performed protein–protein docking for the major haplotypes of NFR5 and K1 receptors in the Schrödinger BioLuminate module. The 30 output complexes passed the first manual selection step with respect to an adequate orientation of complexes to a possible cell membrane. If the putative location of the tra […]

call_split

Immunodominance in T cell responses elicited against different domains of detoxified pneumolysin PlyD1

2018
PLoS One
PMCID: 5839544
PMID: 29509778
DOI: 10.1371/journal.pone.0193650
call_split See protocol

[…] as the template []. The structural coordinates of the template were obtained from the Protein Data Bank []. PlyD1 mutations T65C, G293C and C428A were introduced into the wild-type 3D structure using BioLuminate (Release 2015–3, Schrödinger, LLC, New York, NY, 2015). For each substitution, all residues within a 4 Å cut-off distance from the mutation site were refined in order to accommodate the ne […]

library_books

Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation

2018
Oncotarget
PMCID: 5862610
PMID: 29568389
DOI: 10.18632/oncotarget.24459

[…] eatMusic. The PDB file of NKX2.5-GATA4 complex was prepared and submitted to DrugScorePPI and BeatMusic webserver and the chain of interest was selected for alanine scanning. The residues scanning in BioLuminate was performed through residue scanning/affininty maturation panel in biologics with refinement option set to side-chain prediction and backbone minimization, the cutoff distance was set to […]

call_split

A CK1 FRET biosensor reveals that DDX3X is an essential activator of CK1ε

2018
PMCID: 5818060
PMID: 29222110
DOI: 10.1242/jcs.207316
call_split See protocol

[…] Molecular modeling was performed on a Lenovo ThinkPad T440p (Lenovo) using Schrödinger Suite Maestro (Maestro, version 10.2, Schrödinger, LLC, 2015) and Schrödinger Biologics Suite (BioLuminate, version 1.9, Schrödinger, LLC, 2015). A human DDX3X model was generated based on the high-resolution structure PDB 2I4I (resolution, 2.2 Å) using the protein preparation wizard (standard […]

library_books

Identification of a New Potent Inhibitor Targeting KRAS in Non small Cell Lung Cancer Cells

2017
Front Pharmacol
PMCID: 5694459
PMID: 29184501
DOI: 10.3389/fphar.2017.00823

[…] in the Prep Wiz module of Maestro (Version 9.1, Schrodinger) and water molecules within 5 Å of het groups were kept. Subsequently, the residues of D12 and Q61 were mutated into C12 and H61 using the BioLuminate module of Maestro, respectively. A grid file was generated based on the position of compound BZIM in the Grid Generation wizard. Then, 0375-0604 was prepared to assign atomic charges and g […]

library_books

Functional alterations due to amino acid changes and evolutionary comparative analysis of ARPKD and ADPKD genes

2016
Genom Data
PMCID: 5099264
PMID: 27843768
DOI: 10.1016/j.gdata.2016.10.009

[…] wn. Using computational approach provides binary classifications (impact/neutral) along with a more rational score. Additionally, we get information about the protein's stability through Schrodinger (BioLuminate, USA). In the mutated structure, the mutant residue was targeted in the native protein structure. Many known disease-related nsSNPs in proteins with identified 3D protein structure will ha […]


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BioLuminate institution(s)
BioLuminate, Schrödinger, LLC, New York, NY, USA
BioLuminate funding source(s)
Supported by Schrödinger, Inc.

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