Journal of chemical information and modeling
Oct 3, 2023
With the development of deep learning, almost all single-domain proteins can be predicted at experimental resolution. However, the structure prediction of multi-domain proteins remains a challenge. Achieving end-to-end protein domain assembly and fur...
In this issue of PLOS Biology, Ibrahim and colleagues demonstrate how AlphaFold-multimer, an artificial intelligence-based structure prediction tool, can be used to identify sequence motifs binding to the ATG8 family of proteins central to autophagy.
International journal of molecular sciences
Jan 16, 2023
Drug design with machine learning support can speed up new drug discoveries. While current databases of known compounds are smaller in magnitude (approximately 108), the number of small drug-like molecules is estimated to be between 1023 and 1060. Th...
Chimeric antigen receptor (CAR) costimulatory domains derived from native immune receptors steer the phenotypic output of therapeutic T cells. We constructed a library of CARs containing ~2300 synthetic costimulatory domains, built from combinations ...
The recognition of protein structural folds is the starting point for protein function inference and for many structural prediction tools. We previously introduced the idea of using empirical comparisons to create a data-augmented feature space calle...
The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network mo...
International journal of molecular sciences
Oct 29, 2021
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...
Computational and mathematical methods in medicine
Oct 11, 2021
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 ...
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...
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...
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