Methods of three-dimensional molecular alignment generally treat all pharmacophore features equally when superimposing. However, some pharmacophore features can be more important in a specific system. In this work, we derived the overlap volume of ph...
P-glycoprotein (P-gp) is a transmembrane protein that actively transports a wide variety of chemically diverse compounds out of the cell. It is highly associated with the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties...
Extracting a well-designed energy function is important for protein structure evaluation. Knowledge-based potential functions are one type of the energy functions which can be obtained from known protein structures. The pairwise potential between ato...
Journal of chemical information and modeling
May 15, 2019
A machine learning-based methodology for the prediction of chemical reaction products, along with automated elucidation of mechanistic details via phase space analysis of reactive trajectories, is introduced using low-dimensional heuristic models and...
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through the translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is tightl...
Canonical π-helices are short, relatively unstable secondary structure elements found in proteins. They comprise seven or more residues and are present in 15% of all known protein structures, often in functionally important regions such as ligand- an...
The performance of quantitative structure-activity relationship (QSAR) models largely depends on the relevance of the selected molecular representation used as input data matrices. This work presents a thorough comparative analysis of two main catego...
We have employed our bioinformatics workbench, named Evolution, a Multi-Agent System based architecture with lattice-bead-models, evolutionary-algorithms, and correlated-networks as inhomogeneous spaces, with different correlation lengths, mimicking ...
Journal of chemical information and modeling
Apr 16, 2019
Accurate identification of protein-DNA binding sites is significant for both understanding protein function and drug design. Machine-learning-based methods have been extensively used for the prediction of protein-DNA binding sites. However, the data ...
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