A restricted Boltzmann machine (RBM) is an unsupervised machine learning bipartite graphical model that jointly learns a probability distribution over data and extracts their relevant statistical features. RBMs were recently proposed for characterizi...
We report a self-consistent method to translate amino acid sequences into audible sound, use the representation in the musical space to train a neural network, and then apply it to generate protein designs using artificial intelligence (AI). The soni...
Identification of drug-target interactions (DTIs) plays a key role in drug discovery. The high cost and labor-intensive nature of in vitro and in vivo experiments have highlighted the importance of in silico-based DTI prediction approaches. In severa...
Chemical shifts (CS) are determined from NMR experiments and represent the resonance frequency of the spin of atoms in a magnetic field. They contain a mixture of information, encompassing the in-solution conformations a protein adopts, as well as th...
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...