Journal: Chemical Science

Article Title: Weaver's historic accessible collection of synthetic dyes: a cheminformatics analysis † †The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the US Environmental Protection Agency. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. ‡ ‡Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00567a Click here for additional data file.

doi: 10.1039/c7sc00567a

Figure Lengend Snippet: Circular dendrograms obtained from the hierarchical clustering of the set of 2196 dyes represented in RDKIT descriptor space. Compound nodes & names are colored according to their color (A) and their molecular weight (B).

Article Snippet: 117 2D chemical descriptors were calculated using the RDKIT descriptor calculation node in KNIME.

Techniques: Molecular Weight

Journal: PLOS Neglected Tropical Diseases

Article Title: Design of the Global Health chemical diversity library v2 for screening against infectious diseases

doi: 10.1371/journal.pntd.0011799

Figure Lengend Snippet: (A) Property differences between simple (S) and complex (M), (B) Murcko framework analysis comparing the value of an additional 6,000 complex compounds to an additional 6,000 simple compounds on a base of 24,000 simple compounds. The complex compounds add 15% more Murcko scaffolds and 50% more Murcko frameworks compared to the simple compounds.

Article Snippet: A calculation of the number of unique Murcko [ ] frames done using RDKit as implemented in KNIME 21 using the ‘RDKit Find Murcko Scaffolds’ with the ‘Create Frameworks’ toggle set to OFF.

Techniques:

Journal: Journal of computer-aided molecular design

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings

doi: 10.1007/s10822-018-0180-4

Figure Lengend Snippet: Top 3 submissions, based on Kendall’s τ, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.

Article Snippet: 0.23 , docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome. , J. Sunseri/D. Koes , University of Pittsburgh , vshma.

Techniques: Software

Journal: Journal of computer-aided molecular design

Article Title: D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings

doi: 10.1007/s10822-018-0180-4

Figure Lengend Snippet: Top 3 submissions, based on Matthews correlation coefficient, for each affinity ranking challenge. Submission ID in bold font indicates a method that used machine learning. See for details.

Article Snippet: 0.23 , docking performed with smina static binary available at https//sourceforge.net/projects/smina/files/ with default scoring function, then rescoring performed using gnina commit b3fa6ae13fc6b42924f49b2d751d68f1bc14bc08 available from https//github.com/gnina/gnina and the default cnn scoring model, conformer generation performed with rdkit via https//github.com/dkoes/rdkit-scripts/rdconf.py , ensemble of receptors chosen via pocketome. , J. Sunseri/D. Koes , University of Pittsburgh , vshma.

Techniques: Software