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...
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 ...
Proceedings of the National Academy of Sciences of the United States of America
Jul 6, 2021
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 ...
FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Jan 1, 2021
β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery...
MOTIVATION: Protein domains are subunits that can fold and function independently. Correct domain boundary assignment is thus a critical step toward accurate protein structure and function analyses. There is, however, no efficient algorithm available...
MOTIVATION: Accurate delineation of protein domain boundary plays an important role for protein engineering and structure prediction. Although machine-learning methods are widely used to predict domain boundary, these approaches often ignore long-ran...
MOTIVATION: Domain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based met...
MOTIVATION: Protein-Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by identifying which residues are responsible for the interaction....
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2019
Protein domain boundary prediction is usually an early step to understand protein function and structure. Most of the current computational domain boundary prediction methods suffer from low accuracy and limitation in handling multi-domain types, or ...
MOTIVATION: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processe...
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