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|Interface||Web user interface|
|Restrictions to use||None|
|Input data||Protein/small-molecule complexe(s)|
- person_outline Douglas E. V. Pires
Publication for CSM-lig
Fragment Based Approach to Targeting Inosine 5′ monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis
[…] 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
[…] 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
[…] 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 […]
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