Mutation research. Reviews in mutation research
Mar 23, 2023
Genetic variations are one of the major causes of phenotypic variations between human individuals. Although beneficial as being the substrate of evolution, germline mutations may cause diseases, including Mendelian diseases and complex diseases such ...
Computer methods and programs in biomedicine
Mar 22, 2023
BACKGROUND AND OBJECTIVE: The functions of an organism and its biological processes result from the expression of genes and proteins. Therefore quantifying and predicting mRNA and protein levels is a crucial aspect of scientific research. Concerning ...
The post-genomic era has raised a growing demand for efficient procedures to identify protein functions, which can be accomplished by applying machine learning to the characteristics set extracted from the protein. This approach is feature-based and ...
Current opinion in structural biology
Mar 21, 2023
Computational protein design facilitates the discovery of novel proteins with prescribed structure and functionality. Exciting designs were recently reported using novel data-driven methodologies that can be roughly divided into two categories: evolu...
While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of...
Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large langu...
Noncoding RNA (ncRNA) is a functional RNA derived from DNA transcription, and most transcribed genes are transcribed into ncRNA. ncRNA is not directly involved in the translation of proteins, but it can participate in gene expression in cells and aff...
Journal of chemical information and modeling
Mar 14, 2023
Protein-ligand docking is an essential tool in structure-based drug design with applications ranging from virtual high-throughput screening to pose prediction for lead optimization. Most docking programs for pose prediction are optimized for redockin...
Signal transduction and targeted therapy
Mar 14, 2023
AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most chal...
In tandem mass spectrometry-based proteomics, proteins are digested into peptides by specific protease(s), but generally only a fraction of peptides can be detected. To characterize detectable proteotypic peptides, we have developed a series of metho...