Building Machine Learning Small Molecule Melting Points and Solubility Models Using CCDC Melting Points Dataset.

Predicting solubility of small molecules is a very difficult undertaking due to the lack of reliable and consistent experimental solubility data. It is well known that for a molecule in a crystal lattice to be dissolved, it must, first, dissociate from the lattice and then, second, be solvated. The melting point of a compound is proportional to the lattice energy, and the octanol-water partition coefficient (log ) is a measure of the compound's solvation efficiency.

Indexing Ultrafast Shape-Based Descriptors in MongoDB to Identify TLR4 Pathway Agonists.

A method is presented for an ultrafast shape-based search workflow for the screening of large compound collections, i.e., those of vendors.

All-Assay-Max2 pQSAR: Activity Predictions as Accurate as Four-Concentration ICs for 8558 Novartis Assays.

Profile-quantitative structure-activity relationship (pQSAR) is a massively multitask, two-step machine learning method with unprecedented scope, accuracy, and applicability domain. In step one, a "profile" of conventional single-assay random forest regression models are trained on a very large number of biochemical and cellular pIC assays using Morgan 2 substructural fingerprints as compound descriptors. In step two, a panel of partial least squares (PLS) models are built using the profile of pIC predictions from those random forest regression models as compound descriptors (hence the name).

Profile-QSAR 2.0: Kinase Virtual Screening Accuracy Comparable to Four-Concentration ICs for Realistically Novel Compounds.

While conventional random forest regression (RFR) virtual screening models appear to have excellent accuracy on random held-out test sets, they prove lacking in actual practice. Analysis of 18 historical virtual screens showed that random test sets are far more similar to their training sets than are the compounds project teams actually order. A new, cluster-based "realistic" training/test set split, which mirrors the chemical novelty of real-life virtual screens, recapitulates the poor predictive power of RFR models in real projects.

Enrichment analysis for discovering biological associations in phenotypic screens.

A phenotypic screen (PS) is used to identify compounds causing a desired phenotype in a complex biological system where mechanisms and targets are largely unknown. Deconvoluting the mechanism of action of actives and identification of relevant targets and pathways remains a formidable challenge. Current methods fail to use the rich information available regarding compounds and their targets in a systematic way for this deconvolution.

Web services as applications' integration tool: QikProp case study.

Web services are a new technology that enables to integrate applications running on different platforms by using primarily XML to enable communication among different computers over the Internet. Large number of applications was designed as stand alone systems before the concept of Web services was introduced and it is a challenge to integrate them into larger computational networks. A generally applicable method of wrapping stand alone applications into Web services was developed and is described.

Synthesis, characterization, and molecular structure of a gallium(III) complex of an amine-phenol ligand with activity against chloroquine-sensitive Plasmodium falciparum strains.

Emergence of chloroquine-resistant Plasmodium falciparum strains necessitates discovery of novel antimalarial drugs, especially if the agents can be synthesized from commercially available, inexpensive precursors via short synthetic routes. While exploring structure-activity relationships, we found a gallium(III) complex, [(1,12-bis(2-hydroxy-5-methoxybenzyl)-1,5,8,12-tetraazadodecane)-gallium(III)](+) [Ga-5-Madd](+), 1, that possessed antimalarial efficacy. Like previously reported complexes, the crystal structure of 1 revealed gallium(III) in a symmetrical octahedral environment surrounded by four secondary amine nitrogen atoms in equatorial plane and two axial oxygen atoms.