AIMC Topic: Molecular Structure

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Toward amino acid typing for proteins in FFLUX.

Journal of computational chemistry
Continuing the development of the FFLUX, a multipolar polarizable force field driven by machine learning, we present a modern approach to atom-typing and building transferable models for predicting atomic properties in proteins. Amino acid atomic cha...

BIOLOGICAL AND PHYTOCHEMICAL INVESTIGATIONS OF EXTRACTS FROM POIR (FABACEAE) ROOT BARKS.

African journal of traditional, complementary, and alternative medicines : AJTCAM
BACKGROUND: Poir. belonging to Fabacae familly is used as medicinal plant in Burkina Faso's folk medicine. Roots of are used to treat ulcer, stomach ache and inflammatory diseases. The objective of the present study was to carry out phytochemical c...

Prediction of blood-brain barrier permeability of organic compounds.

Doklady. Biochemistry and biophysics
Using fragmental descriptors and artificial neural networks, a predictive model of the relationship between the structure of organic compounds and their blood-brain barrier permeability was constructed and the structural factors affecting the readine...

QSPR studies for predicting polarity parameter of organic compounds in methanol using support vector machine and enhanced replacement method.

SAR and QSAR in environmental research
In the present work, enhanced replacement method (ERM) and support vector machine (SVM) were used for quantitative structure-property relationship (QSPR) studies of polarity parameter (p) of various organic compounds in methanol in reversed phase liq...

A knowledge-based expert rule system for predicting mutagenicity (Ames test) of aromatic amines and azo compounds.

Toxicology
Cancer is one of the main causes of death in Western countries, and a major issue for human health. Prolonged exposure to a number of chemicals was observed to be one of the primary causes of cancer in occupationally exposed persons. Thus, the develo...

Machine Learning Prediction of the Energy Gap of Graphene Nanoflakes Using Topological Autocorrelation Vectors.

ACS combinatorial science
The possibility of band gap engineering in graphene opens countless new opportunities for application in nanoelectronics. In this work, the energy gaps of 622 computationally optimized graphene nanoflakes were mapped to topological autocorrelation ve...

ROCS-derived features for virtual screening.

Journal of computer-aided molecular design
Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to combine many aspects of similarity, yielding parameter-free models for virtual screening. I...

Molecular graph convolutions: moving beyond fingerprints.

Journal of computer-aided molecular design
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structur...

Developing a support vector machine based QSPR model for prediction of half-life of some herbicides.

Ecotoxicology and environmental safety
The half-life (t1/2) of 58 herbicides were modeled by quantitative structure-property relationship (QSPR) based molecular structure descriptors. After calculation and the screening of a large number of molecular descriptors, the most relevant those o...