Intrinsically disordered proteins have dynamic structures through which they play key biological roles. The elucidation of their conformational ensembles is a challenging problem requiring an integrated use of computational and experimental methods. ...
Journal of chemical information and modeling
May 17, 2024
The atomic partial charge is of great importance in many fields, such as chemistry and drug-target recognition. However, conventional quantum-based computing of atomic charges is relatively slow, limiting further applications of atomic charge analysi...
Current opinion in structural biology
May 13, 2024
Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of protein complexes, and the regulation of biological functional processes. Classical simulation methods c...
Journal of chemical information and modeling
May 13, 2024
Currently, antimicrobial resistance constitutes a serious threat to human health. Drugs based on antimicrobial peptides (AMPs) constitute one of the alternatives to address it. Shallow and deep learning (DL)-based models have mainly been built from a...
The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them approp...
The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design. Here we describe our AlphaFold 3 model with a substantially...
Interdisciplinary sciences, computational life sciences
May 6, 2024
Molecular representation learning can preserve meaningful molecular structures as embedding vectors, which is a necessary prerequisite for molecular property prediction. Yet, learning how to accurately represent molecules remains challenging. Previou...
Journal of chemical information and modeling
May 6, 2024
Developing new pharmaceuticals is a costly and time-consuming endeavor fraught with significant safety risks. A critical aspect of drug research and disease therapy is discerning the existence of interactions between drugs and proteins. The evolution...
The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structu...
Journal of computer-aided molecular design
May 1, 2024
Covalent inhibition offers many advantages over non-covalent inhibition, but covalent warhead reactivity must be carefully balanced to maintain potency while avoiding unwanted side effects. While warhead reactivities are commonly measured with assays...