Journal of chemical information and modeling
Nov 7, 2022
Molecular docking tools are regularly used to computationally identify new molecules in virtual screening for drug discovery. However, docking tools suffer from inaccurate scoring functions with widely varying performance on different proteins. To en...
As a potential and effective substitute for the drugs of antihypertension, the food-derived antihypertensive peptides have arisen great interest in scholars recently. However, the traditional screening methods for antihypertensive peptides are at con...
In the recent COVID-19 pandemic, SARS-CoV-2 infection spread worldwide. The 3C-like protease (3CLpro) is a promising drug target for SARS-CoV-2. We constructed a deep learning-based convolutional neural network-quantitative structure-activity relat...
Journal of chemical information and modeling
Sep 26, 2022
Computational methods for virtual screening can dramatically accelerate early-stage drug discovery by identifying potential hits for a specified target. Docking algorithms traditionally use physics-based simulations to address this challenge by estim...
Journal of chemical information and modeling
Sep 9, 2022
Water molecules at the ligand-protein interfaces play crucial roles in the binding of the ligands, but the behavior of protein-bound water is largely ignored in many currently used machine learning (ML)-based scoring functions (SFs). In an attempt to...
In this article, the upgrading process of the structure-based virtual screening (SBVS) protocol targeting acetylcholinesterase (AChE) previously published in 2017 is presented. The upgraded version of PyPLIF called PyPLIF HIPPOS and the receptor ense...
The outbreak of COVID-19 caused millions of deaths worldwide, and the number of total infections is still rising. It is necessary to identify some potentially effective drugs that can be used to prevent the development of severe symptoms, or even dea...
The binding of small organic molecules to protein targets is fundamental to a wide array of cellular functions. It is also routinely exploited to develop new therapeutic strategies against a variety of diseases. On that account, the ability to effect...
INTRODUCTION: The discovery of a new drug is a costly and lengthy endeavour. The computational prediction of which small molecules can bind to a protein target can accelerate this process if the predictions are fast and accurate enough. Recent machin...
Identifying native-like protein-ligand complexes (PLCs) from an abundance of docking decoys is critical for large-scale virtual drug screening in early-stage drug discovery lead searching efforts. Providing reliable prediction is still a challenge fo...
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