BACKGROUND: Cysteine-dense peptides (CDPs) are an attractive pharmaceutical scaffold that display extreme biochemical properties, low immunogenicity, and the ability to bind targets with high affinity and selectivity. While many CDPs have potential a...
For most proteins annotated as enzymes, it is unknown which primary and/or secondary reactions they catalyze. Experimental characterizations of potential substrates are time-consuming and costly. Machine learning predictions could provide an efficien...
Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, and when elucidating the molecular mechanisms behind evolution and disease. Here, we present RaSP, a method for making rapid and accurate pred...
Journal of chemical information and modeling
May 11, 2023
The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide intera...
Journal of chemical information and modeling
May 11, 2023
Over the past few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input and outputs th...
Journal of chemical information and modeling
May 9, 2023
Noncoding RNAs (ncRNAs) play crucial roles in many cellular life activities by interacting with proteins. Identification of ncRNA-protein interactions (ncRPIs) is key to understanding the function of ncRNAs. Although a number of computational methods...
Machine learning research concerning protein structure has seen a surge in popularity over the last years with promising advances for basic science and drug discovery. Working with macromolecular structure in a machine learning context requires an ad...
Recently it has become possible to de novo design high affinity protein binding proteins from target structural information alone. There is, however, considerable room for improvement as the overall design success rate is low. Here, we explore the au...
Journal of chemical information and modeling
May 5, 2023
pH regulates protein structures and the associated functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibria are determined by p's. To accelerate pH-dependent molecular mechanism ...
Macromolecular assemblies play an important role in all cellular processes. While there has recently been significant progress in protein structure prediction based on deep learning, large protein complexes cannot be predicted with these approaches. ...