CSM-lig statistics

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CSM-lig specifications

Web

Information

Unique identifier	OMICS_12055
Name	CSM-lig
Interface	Web user interface
Restrictions to use	None
Input data	Protein/small-molecule complexe(s)
Input format	PDB
Computer skills	Basic
Stability	Stable
Maintained	Yes

Maintainer

Douglas E. V. Pires

Publication for CSM-lig

CSM-lig: a web server for assessing and comparing protein–small molecule affinities

2016 Nucleic Acids Res

PMCID: 4987933

PMID: 27151202

DOI: 10.1093/nar/gkw390

CSM-lig citations

(3)

Fragment Based Approach to Targeting Inosine 5′ monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis

2018

J Med Chem

PMCID: 5900554

PMID: 29547284

DOI: 10.1021/acs.jmedchem.7b01622

[…] enix, and the structures were manually refined further using Coot. Information regarding the crystallographic statistics can be found in . Protein–ligand interactions were analyzed using Arpeggio and CSM-Lig., Compound properties were evaluated using pkCSM. All figures made using Pymol (Schrodinger). […]

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

2016

J Am Chem Soc

PMCID: 5253712

PMID: 28009512

DOI: 10.1021/jacs.6b11467

[…] d out in Gromacs 5.0.4 or Gromacs 5.1. 10 000 energy minimization steps were performed using a steepest descent algorithm (the protein–ligand structures obtained after this step were submitted to the CSM-Lig server for scoring). The system was subsequently simulated for 0.5 ns in the canonical ensemble and for 1 ns in the isothermal–isobaric ensemble with harmonic position restraints applied to al […]

The Presence, Persistence and Functional Properties of Plasmodium vivax Duffy Binding Protein II Antibodies Are Influenced by HLA Class II Allelic Variants

2016

PLoS Negl Trop Dis

PMCID: 5154503

PMID: 27959918

DOI: 10.1371/journal.pntd.0005177

[…] KLYLKRKL; H3: DEKAQQRRKQWWNESK) were modelled into each HLA II complex variant using the available crystal structures of the HLA II complexes to guide docking. Binding affinities were predicted using CSM-lig []. Model structures were examined using Pymol.The structural consequences of each amino acid difference between the DRB1 variants were analyzed to account for all the potential effects of the […]

Citations

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CSM-lig institution(s)

Centro de Pesquisas Rene Rachou, Fundacao Oswaldo Cruz, Belo Horizonte, Brazil; Department of Biochemistry, University of Cambridge, Cambridge, UK; Department of Biochemistry, University of Melbourne, Victoria, Australia

CSM-lig funding source(s)

Newton Fund RCUK-CONFAP Grant awarded by The Medical Research Council and Fundacao de Amparo a Pesquisa do Estado de Minas Gerais ; Rene Rachou Research Center (CPqRR/FIOCRUZ Minas), Brazil; NHMRC CJ Martin Fellowship [APP1072476].

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