BACKGROUND: DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein-DNA interfaces. As experimental methods for identifying hot spots are time-consuming...
Journal of biomolecular structure & dynamics
May 6, 2021
It is familiar that essential proteins take part in managing cellular activities in living organisms. Moreover, protein structure prediction from its amino acid sequence is advantageous to the comprehending of cellular functions. Formerly, several es...
Computational generation of new proteins with a predetermined three-dimensional shape and computational optimization of existing proteins while maintaining their shape are challenging problems in structural biology. Here, we present a protocol that u...
Proteins are one of the most important molecules that govern the cellular processes in most of the living organisms. Various functions of the proteins are of paramount importance to understand the basics of life. Several supervised learning approache...
Identifying the interactions of the drug-target is central to the cognate areas including drug discovery and drug reposition. Although the high-throughput biotechnologies have made tremendous progress, the indispensable clinical trials remain to be e...
Despite the availability of methods for analyzing protein complexes, systematic analysis of complexes under multiple conditions remains challenging. Approaches based on biochemical fractionation of intact, native complexes and correlation of protein ...
International journal of molecular sciences
Apr 14, 2021
Accurate prediction of binding affinity between protein and ligand is a very important step in the field of drug discovery. Although there are many methods based on different assumptions and rules do exist, prediction performance of protein-ligand bi...
Inferring a phylogenetic tree is a fundamental challenge in evolutionary studies. Current paradigms for phylogenetic tree reconstruction rely on performing costly likelihood optimizations. With the aim of making tree inference feasible for problems i...
Advances in protein chemistry and structural biology
Mar 24, 2021
With the tremendous developments in the fields of biological and medical technologies, huge amounts of data are generated in the form of genomic data, images in medical databases or as data on protein sequences, and so on. Analyzing this data through...
Microbial rhodopsins are photoreceptive membrane proteins, which are used as molecular tools in optogenetics. Here, a machine learning (ML)-based experimental design method is introduced for screening rhodopsins that are likely to be red-shifted from...