Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, and when elucidating the molecular mechanisms behind evolution and disease. Here, we present RaSP, a method for making rapid and accurate pred...
Biochimica et biophysica acta. Molecular basis of disease
Apr 25, 2023
Understanding the molecular basis and impact of mutations at different stages of cancer are long-standing challenges in cancer biology. Identification of driver mutations from experiments is expensive and time intensive. In the present study, we coll...
"Newly Born" proteins, devoid of detectable homology to any other proteins, known as orphan proteins, occur in a single species or within a taxonomically restricted gene family. They are generated by the expression of novel open reading frames, and a...
We present a deep-learning-based platform, MIND-S, for protein post-translational modification (PTM) predictions. MIND-S employs a multi-head attention and graph neural network and assembles a 15-fold ensemble model in a multi-label strategy to enabl...
Journal of bioinformatics and computational biology
Mar 9, 2023
Protein secondary structure prediction (PSSP) is an important and challenging task in protein bioinformatics. Protein secondary structures (SSs) are categorized in regular and irregular structure classes. Regular SSs, representing nearly 50% of amino...
Journal of bioinformatics and computational biology
Feb 10, 2023
This work proposes a machine learning-based phylogenetic tree generation model based on agglomerative clustering (PTGAC) that compares protein sequences considering all known chemical properties of amino acids. The proposed model can serve as a suita...
Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap b...
Current sequence-based predictors of protein-binding residues (PBRs) belong to two distinct categories: structure-trained vs. intrinsic disorder-trained. Since disordered PBRs differ from structured PBRs in several ways, including ability to bind mul...
Protein 3-hydroxyl-3-methylglutarylation (HMGylation) is newly discovered lysine acylation modification in mitochondrion. The accurate identification of HMGylation sites is the premise and key to further explore the molecular mechanisms of HMGylation...
MOTIVATION: Proteins-protein interactions (PPIs) are important to govern several cellular activities. Amino acid residues, which are located at the interface are known as the binding sites and the information about binding sites helps to understand t...
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