chemaxon calculator plugin (ChemAxon LLC)

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ChemAxon LLC chemaxon calculator plugin
Chemaxon Calculator Plugin, supplied by ChemAxon LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/chemaxon+calculator+plugins/chemaxon+calculator+plugins/pmc11278217-133-1-1
Average 90 stars, based on 1 article reviews

chemaxon calculator plugin - by Bioz Stars, 2026-11

90/100 stars

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Activity Assay:

Article Title: Design, synthesis and biological evaluation of novel cyclic malonamide derivatives as selective RIPK1 inhibitors.
Article Snippet: Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) plays a key role in cell death and inflammation.. RIPK1 is a well-established therapeutic target, due to the presence of a unique kinase-regulating allosteric pocket, which enables selective inhibition.. Herein we used GSK2982772 as our starting point in our discovery campaign.

Kinase Assay:

Inhibition:

other:

Article Title: A big data approach to the ultra-fast prediction of DFT-calculated bond energies
Article Snippet: The ChemAxon Calculator Plugins were used to generate 3D structures from SMILES strings, and to propose low energy conformers for structure property prediction and calculation, Marvin 5.8.2, 2012, ChemAxon ( http://www.chemaxon.com ) [ ] was employed.

Article Title: A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors
Article Snippet: A "3D" sdf version was prepared for docking using an in-house automated pipeline performing: Chemical standardization and curation (ChEMBL protocols [56]); Removal of chemical duplicates (Open Babel [57]); Selection of dominant tautomers (pH 7.4, ChemAxon Calculator Plugins version 19.0.9, https://chemaxon.com); Selection of species populating more than 25% or, if none, species that are present at more than 75% of the most frequent one, or at least the three most frequent ones; Generation of stereoisomers and low energy ring conformers generation (CORINA classic [58] version 3.4, https://www.mn-am.com); Slight minimization (RDKit version 2018.03.4, https://www.rdkit.org); Annotation and flagging for solubility (ChemAxon Calculator Plugins), and for toxicophores, “Pan Assay Interference Compounds” (PAINS) [59], "Solubility Forecast Index" [60], "Quantitative Estimate of Drug-likeness" (QED) [61], and the Veber rule ([62], implemented in an in-house script using RDKit).

Article Title: A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors
Article Snippet: A “3D” sdf version was prepared for docking using an in-house automated pipeline performing: Chemical standardization and curation (ChEMBL protocols [ ]); Removal of chemical duplicates (Open Babel [ ]); Selection of dominant tautomers (pH 7.4, ChemAxon Calculator Plugins version 19.0.9, https://chemaxon.com ); Selection of species populating more than 25% or, if none, species that are present at more than 75% of the most frequent one, or at least the three most frequent ones; Generation of stereoisomers and low energy ring conformers generation (CORINA classic [ ] version 3.4, https://www.mn-am.com ); Slight minimization (RDKit version 2018.03.4, https://www.rdkit.org ); Annotation and flagging for solubility (ChemAxon Calculator Plugins), and for toxicophores, “Pan Assay Interference Compounds” (PAINS) [ ], “Solubility Forecast Index” [ ], “Quantitative Estimate of Drug-likeness” (QED) [ ], and the Veber rule ([ ], implemented in an in-house script using RDKit).

Expressing:

Article Title: Probing Bioactive Chemical Space to Discover RNA-Targeted Small Molecules
Article Snippet: .. Using the ChemAxon Calculator Plugins, ligands were corrected to their major protonation and tautomeric states (pH = 7.4), and then the 20 cheminformatic parameters were calculated using the ChemAxon Chemical Terms Evaluator (Marvin 16.4.25.0, 2016, http://www.chemaxon.com) (SI Table 1).1 SI Table 1: Cheminformatic descriptors Category Parameter Description Chemical Terms Evaluator Expression Medicinal chemistry MW Molecular weight mass() HBA Number of hydrogen bond acceptors acceptorCount() HBD Number of hydrogen bond donors donorCount() LogP n-Octanol/Water partition coefficient logPKLOP() RotB Number of rotatable bonds rotatableBondCount() tPSA Topological polar surface area PSA() LogD n-Octanol/Water distribution coefficient logD(‘7.4’) Structural N Number of nitrogen atoms atomCount(‘7’) O Number of oxygen atoms atomCount(‘8’) Rings Number of rings ringCount() ArRings Number of aromatic rings aromaticRingCount() HetRings Number of heteroatomcontaining rings heteroRingCount() SysRings Number of ring systems ringSystemCount() SysRR Ring complexity ringCount()/ringSystemCount() Molecular complexity & recognition Fsp3 Fraction of sp3 hybridized carbons Count(filter(‘atno()==6&&connections()==4’))/atomCount(‘6’) nStereo Number of stereocenters chiralCenterCount() ASA Accessible surface area ASA() relPSA Relative polar surface area PSA()/vanDerWaalsSurfaceArea() TC Total charge totalCharge() VWSA van der Waals surface area vanDerWaalsSurfaceArea() S4 SI-2. .. Nearest Neighbor Search A k-Nearest neighbors algorithm was used, where k = 1, to evaluate overlap between pairs of small molecules.2, 3 The nearest neighbor distance for R-BIND (SM) v1.1 was calculated by: (1) Normalizing each cheminformatic parameter of every small molecule to the mean and standard deviation of the descriptor for the library; (2) Using the normalized values to calculate multidimensional distances in space between each pair of R-BIND (SM) ligands; (3) Averaging the smallest nearest neighbor distance (d) for each R-BIND (SM); and (4) Mapping each R-BIND (SM) as a multi-dimensional sphere with a radius of d. Similarly, commercial ligands from ChemBridge (n = 1,146,666) and ChemDiv (n = 1,465,277) were normalized to the R-BIND (SM) v1.1 library and mapped as a multi-dimensional sphere with a radius of the smallest averaged nearest neighbor distance.

Molecular Weight:

Generated:

Article Title: Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9
Article Snippet: .. The 3D compound structures were generated using the freely available web server Frog2 [ ], and the compounds were protonated at pH 7.4 using the major macrospecies option of the ChemAxon calculator plugins ( www.chemaxon.com ). ..

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