In Dec 2020, the results of AlphaFold version 2 were presented at CASP14, sparking a
revolution in the field of protein structure predictions. For the first time, a purely …

The advent of advanced molecular modeling software, big data analytics, and high-speed
processing units has led to the exponential evolution of modern drug discovery and better …

In the current era of modern drug design & development via computer-aided drug design,
the potential role of computational software tools is widely enlarged in use. Computer-based …

RNA-protein (RNP) interactions play essential roles in many biological processes, such as
regulation of co-transcriptional and post-transcriptional gene expression, RNA splicing …

Protein–protein docking technology is an effective approach to study the molecular
mechanism of essential biological processes mediated by complex protein–protein …

We present a novel optimization approach to train a free-shape distance-dependent protein-
ligand scoring function called Convex-PL. We do not impose any functional form of the …

Predicting the quaternary structure of protein complex is an important problem. Inter‐chain
residue‐residue contact prediction can provide useful information to guide the ab initio …

Molecular docking is critical to structure-based virtual screening, yet the throughput of such
workflows is limited by the expensive optimization of scoring functions involved in most …

Protein-RNA interactions play an important role in many biological processes.
Computational methods such as docking have been developed to complement existing …

Motivation The root mean square deviation (RMSD) is one of the most used similarity criteria
in structural biology and bioinformatics. Standard computation of the RMSD has a linear …