MedusaScore statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MedusaScore
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Tool usage distribution map

This map represents all the scientific publications referring to MedusaScore per scientific context
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Popular tool citations

chevron_left Ligand-based virtual screening Protein-ligand docking chevron_right
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Protocols

MedusaScore specifications

Information


Unique identifier OMICS_19939
Name MedusaScore

Maintainer


This tool is not maintained anymore.

Publication for MedusaScore

MedusaScore citations

 (5)
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Star Polymers Reduce Islet Amyloid Polypeptide Toxicity via Accelerated Amyloid Aggregation

2017
PMCID: 5729549
PMID: 29035554
DOI: 10.1021/acs.biomac.7b01301
call_split See protocol

[…] yzing all the independent runs for each molecular system.All the PHEA model structures were constructed with the Avogadro molecular builder software and energy minimized with the MMFF94s force field. MedusaScore, an extension of the Medusa force field, was adapted to model the polymers in addition to IAPP. The MedusaScore was parametrized on a large set of ligands and was transferrable to differen […]

library_books

Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

2016
Sci Rep
PMCID: 5109037
PMID: 27845442
DOI: 10.1038/srep37175

[…] k comprises a docking step intertwined with a scoring step, where the docking step creates a ligand rotamer library and searches the best fit within the flexible side chain rotamer library, using the MedusaScore force field. We select the final candidates through ranking the 21 candidates by best-predicted binding energy (). We find this method of ranking reveals a natural division between the can […]

call_split

Differential Regulation of 6 and 7 Transmembrane Helix Variants of μ Opioid Receptor in Response to Morphine Stimulation

2015
PLoS One
PMCID: 4640872
PMID: 26554831
DOI: 10.1371/journal.pone.0142826
call_split See protocol

[…] tion of the 7TM-mOR binding site in complex with the antagonist β-FNA. During docking, we retrieve representative conformations of morphine in complex with 7TM- and 6TM-mOR by combining the values of MedusaScore [], a physical force field based scoring function accounting for the protein-ligand interaction energy, with a hierarchical cluster analysis of the top-ranked ligand conformations. In furt […]

library_books

COMT gene locus: new functional variants

2015
PMCID: 4748386
PMID: 26207649
DOI: 10.1097/j.pain.0000000000000273

[…] cocrystallized 3,5-dinitrocatechol with a ligand root-mean-square deviation of 0.43 Å.Furthermore, we evaluated the binding affinity of SAM using our in-house developed physics-based scoring function MedusaScore for the 2 COMT isoforms, S- and (a)S-COMT. We retained the crystallographic coordinates of Mg2+, OW, 3,5-dinitrocatechol, and water molecules localized in SAM-binding site of S-COMT. Also, […]

call_split

Competitive Binding of Natural Amphiphiles with Graphene Derivatives

2013
Sci Rep
PMCID: 3721079
PMID: 23881402
DOI: 10.1038/srep02273
call_split See protocol

[…] e non-planner after the energy minimization ().The molecular structures of cellulose dimer, tri-alanine and palmitic acid were generated and minimized using open babel (openbabel.org). We adapted the MedusaScore force field, an extended Medusa force field for small-molecule ligands, to model the inter-atomic interactions of biomolecules beyond proteins. […]


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MedusaScore institution(s)
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic; Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
MedusaScore funding source(s)
Supported by National Institutes of Health (Grant No. RO1-GM080742).

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