Journal of chemical information and modeling
Sep 26, 2022
Directed evolution, a revolutionary biotechnology in protein engineering, optimizes protein fitness by searching an astronomical mutational space via expensive experiments. The cluster learning-assisted directed evolution (CLADE) efficiently explores...
International journal of molecular sciences
Sep 22, 2022
The prediction of the strengths of drug-target interactions, also called drug-target binding affinities (DTA), plays a fundamental role in facilitating drug discovery, where the goal is to find prospective drug candidates. With the increase in the nu...
Molecules (Basel, Switzerland)
Sep 19, 2022
Proteins are the fundamental biological macromolecules which underline practically all biological activities. Protein-protein interactions (PPIs), as they are known, are how proteins interact with other proteins in their environment to perform biolog...
PLoS computational biology
Sep 16, 2022
Despite the immense progress recently witnessed in protein structure prediction, the modeling accuracy for proteins that lack sequence and/or structure homologs remains to be improved. We developed an open-source program, DeepFold, which integrates s...
Science (New York, N.Y.)
Sep 15, 2022
Although deep learning has revolutionized protein structure prediction, almost all experimentally characterized de novo protein designs have been generated using physically based approaches such as Rosetta. Here, we describe a deep learning-based pro...
Journal of chemical information and modeling
Sep 15, 2022
Molecular surface representations have been advertised as a great tool to study protein structure and functions, including protein-ligand binding affinity modeling. However, the conventional surface-area-based methods fail to deliver a competitive pe...
IEEE transactions on pattern analysis and machine intelligence
Sep 14, 2022
Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models (LMs) taken from Natural Language Processing (NLP). These LMs reach for new prediction frontiers at low inference costs. Here, we ...
Methods (San Diego, Calif.)
Sep 13, 2022
Non-coding RNA (ncRNA) s play an considerable role in the current biological sciences, such as gene transcription, gene expression, etc. Exploring the ncRNA-protein interactions(NPI) is of great significance, while some experimental techniques are ve...
Journal of chemical information and modeling
Sep 13, 2022
The availability of AlphaFold2 has led to great excitement in the scientific community─particularly among drug hunters─due to the ability of the algorithm to predict protein structures with high accuracy. However, beyond globally accurate protein str...
Bioorganic & medicinal chemistry
Sep 9, 2022
Prediction of protein-ligand binding affinities is crucial for computational drug discovery. A number of deep learning approaches have been developed in recent years to improve the accuracy of such affinity prediction. While the predicting power of t...