I outline how over my career as a protein scientist Machine Learning has impacted my area of science and one of my pastimes, chess, where there are some interesting parallels. In 1968, modelling of three-dimensional structures was initiated based on ...
Single-molecule force spectroscopy has become a powerful tool for the exploration of dynamic processes that involve proteins; yet, meaningful interpretation of the experimental data remains challenging. Owing to low signal-to-noise ratio, experimenta...
: Structure-guided drug discovery relies on accurate computational methods for modeling macromolecules. Simulations provide means of predicting macromolecular folds, of discovering function from structure, and of designing macromolecules to serve as ...
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main challenges in computational biology and chemistry. Predicting any protein's accurate structure is of paramount importance for the scientific community, as the...
Lysine succinylation is a typical protein post-translational modification and plays a crucial role of regulation in the cellular process. Identifying succinylation sites is fundamental to explore its functions. Although many computational methods wer...
As more bioactivity and protein structure data become available, scoring functions (SFs) using machine learning (ML) to leverage these data sets continue to gain further accuracy and broader applicability. Advances in our understanding of the optimal...
Journal of chemical information and modeling
May 26, 2021
RNA three-dimensional structure prediction has been relied on using a predicted or experimentally determined secondary structure as a restraint to reduce the conformational sampling space. However, the secondary-structure restraints are limited to pa...
The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for predicting pro...
International journal of molecular sciences
May 24, 2021
Obtaining an accurate description of protein structure is a fundamental step toward understanding the underpinning of biology. Although recent advances in experimental approaches have greatly enhanced our capabilities to experimentally determine prot...
BACKGROUND: Post-translational modification (PTM) is a biological process that alters proteins and is therefore involved in the regulation of various cellular activities and pathogenesis. Protein phosphorylation is an essential process and one of the...