iProt-Sub: a comprehensive package for accurately map** and predicting protease-specific substrates and cleavage sites
Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The
key to better understanding the mechanisms that control this process is to identify the …
key to better understanding the mechanisms that control this process is to identify the …
A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states
Solvent accessible surface area (SASA) of proteins has always been considered as a
decisive factor in protein folding and stability studies. It is defined as the surface …
decisive factor in protein folding and stability studies. It is defined as the surface …
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction
Predicting the functional sites of a protein from its structure, such as the binding sites of small
molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two …
molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two …
Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone …
Motivation The accuracy of predicting protein local and global structural properties such as
secondary structure and solvent accessible surface area has been stagnant for many years …
secondary structure and solvent accessible surface area has been stagnant for many years …
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites
The ability to catalytically cleave protein substrates after synthesis is fundamental for all
forms of life. Accordingly, site-specific proteolysis is one of the most important post …
forms of life. Accordingly, site-specific proteolysis is one of the most important post …
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
The rapid accumulation of molecular data motivates development of innovative approaches
to computationally characterize sequences, structures and functions of biological and …
to computationally characterize sequences, structures and functions of biological and …
[HTML][HTML] Protein representations: Encoding biological information for machine learning in biocatalysis
D Harding-Larsen, J Funk, NG Madsen… - Biotechnology …, 2024 - Elsevier
Enzymes offer a more environmentally friendly and low-impact solution to conventional
chemistry, but they often require additional engineering for their application in industrial …
chemistry, but they often require additional engineering for their application in industrial …
PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework
Determining the catalytic residues in an enzyme is critical to our understanding the
relationship between protein sequence, structure, function, and enhancing our ability to …
relationship between protein sequence, structure, function, and enhancing our ability to …
Single‐sequence‐based prediction of protein secondary structures and solvent accessibility by deep whole‐sequence learning
Predicting protein structure from sequence alone is challenging. Thus, the majority of
methods for protein structure prediction rely on evolutionary information from multiple …
methods for protein structure prediction rely on evolutionary information from multiple …
Enhanced prediction of hot spots at protein-protein interfaces using extreme gradient boosting
H Wang, C Liu, L Deng - Scientific reports, 2018 - nature.com
Identification of hot spots, a small portion of protein-protein interface residues that contribute
the majority of the binding free energy, can provide crucial information for understanding the …
the majority of the binding free energy, can provide crucial information for understanding the …