Journal of bioinformatics and computational biology
Sep 19, 2018
Protein Function Prediction from Protein-Protein Interaction Network (PPIN) and physico-chemical features using the Gene Ontology (GO) classification are indeed very useful for assigning biological or biochemical functions to a protein. They also lea...
International journal of molecular sciences
Sep 18, 2018
Protein hydroxylation is one type of post-translational modifications (PTMs) playing critical roles in human diseases. It is known that protein sequence contains many uncharacterized residues of proline and lysine. The question that needs to be answe...
Journal of chemical information and modeling
Aug 29, 2018
It has been long established that cis conformations of amino acid residues play many biologically important roles despite their rare occurrence in protein structure. Because of this rarity, few methods have been developed for predicting cis isomers f...
Journal of chemical theory and computation
Aug 17, 2018
The ability to accurately and efficiently compute quantum-mechanical partial atomistic charges has many practical applications, such as calculations of IR spectra, analysis of chemical bonding, and classical force field parametrization. Machine learn...
Mathematical biosciences
Aug 14, 2018
Understanding proteins, their structures, functions, mutual interactions, activity in cellular reactions, interactions with drugs, and expression in body cells is a key to efficient medical diagnosis, drug production, and treatment of patients. Machi...
Journal of computational biology : a journal of computational molecular cell biology
Jul 27, 2018
Recently, the number of the amino acid sequences shared in online databases is growing rapidly in huge amounts. By using sequence-derived features, machine learning algorithms are successfully applied to prediction of protein functional classes, prot...
Scientific reports
Jul 26, 2018
Protein S-sulfenylation, which results from oxidation of free thiols on cysteine residues, has recently emerged as an important post-translational modification that regulates the structure and function of proteins involved in a variety of physiologic...
BMC medical informatics and decision making
Jul 23, 2018
BACKGROUND: Relationships between bio-entities (genes, proteins, diseases, etc.) constitute a significant part of our knowledge. Most of this information is documented as unstructured text in different forms, such as books, articles and on-line pages...
BMC bioinformatics
Jul 18, 2018
BACKGROUND: Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Ami...
Scientific reports
Jun 29, 2018
Protein secondary structure prediction is one of the most important and challenging problems in bioinformatics. Machine learning techniques have been applied to solve the problem and have gained substantial success in this research area. However ther...