Computational and mathematical methods in medicine
34671418
Membrane protein is an important kind of proteins. It plays essential roles in several cellular processes. Based on the intramolecular arrangements and positions in a cell, membrane proteins can be divided into several types. It is reported that the ...
Journal of chemical theory and computation
34161735
Protein domains are independent, functional, and stable structural units of proteins. Accurate protein domain boundary prediction plays an important role in understanding protein structure and evolution, as well as for protein structure prediction. C...
Interdisciplinary sciences, computational life sciences
34236625
BACKGROUND: Prediction of protein solubility is an indispensable prerequisite for pharmaceutical research and production. The general and specific objective of this work is to design a new model for predicting protein solubility by using protein sequ...
Proceedings of the National Academy of Sciences of the United States of America
34187888
Recent progress in DNA synthesis and sequencing technology has enabled systematic studies of protein function at a massive scale. We explore a deep mutational scanning study that measured the transcriptional repression function of 43,669 variants of ...
Domains are instrumental in facilitating protein interactions with DNA, RNA, small molecules, ions and peptides. Identifying ligand-binding domains within sequences is a critical step in protein function annotation, and the ligand-binding properties ...
Peptide-protein interactions are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. Recently, a number of computational methods have been developed to predict peptide...
International journal of molecular sciences
34769173
Computational Protein Design (CPD) has produced impressive results for engineering new proteins, resulting in a wide variety of applications. In the past few years, various efforts have aimed at replacing or improving existing design methods using De...
The MANORAA platform uses structure-based approaches to provide information on drug design originally derived from mapping tens of thousands of amino acids on a grid. In-depth analyses of the pockets, frequently occurring atoms, influential distances...
Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However...
MOTIVATION: Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural...