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Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of classical algorithms have been developed to carry out…
Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being…
Antibodies are canonically Y-shaped multimeric proteins capable of highly specific molecular recognition. The CDRH3 region located at the tip of variable chains of an antibody dominates antigen-binding specificity. Therefore, it is a…
Biomolecular condensates, physically underpinned to a significant extent by liquid-liquid phase separation (LLPS), are now widely recognized by numerous experimental studies to be of fundamental biological, biomedical, and biophysical…
High throughput screening of small molecules and natural products is costly, requiring significant amounts of time, reagents, and operating space. Although microarrays have proven effective in the miniaturization of screening for certain…
In drug discovery, aqueous solubility is an important pharmacokinetic property which affects absorption and assay availability of drug. Thus, in silico prediction of solubility has been studied for its utility in virtual screening and lead…
One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
Lampreys are jawless fish that evolved about 550 million years ago at the base of the vertebrate line. Modern lampreys contain a corticoid receptor (CR), the common ancestor of the glucocorticoid receptor (GR) and mineralocorticoid receptor…
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences…
Multi-task learning for molecular property prediction is becoming increasingly important in drug discovery. However, in contrast to other domains, the performance of multi-task learning in drug discovery is still not satisfying as the…
Cryogenic electron microscopy (cryo-EM) provides a unique opportunity to study the structural heterogeneity of biomolecules. Being able to explain this heterogeneity with atomic models would help our understanding of their functional…
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property, where design of novel drugs is an important topic in bioinformatics and chemo-informatics. The…
Virus infection is one of the major diseases that seriously threaten human health. To meet the growing demand for mining and sharing data resources related to antiviral drugs and to accelerate the design and discovery of new antiviral…
As antibiotic-resistant bacterial strains are rapidly spreading worldwide, infections caused by these strains are emerging as a global crisis causing the death of millions of people every year. Antimicrobial Peptides (AMPs) are one of the…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…