We develop a machine learning tool useful for predicting the instantaneous dynamical state of sub-monomer features within long linear polymer chains, as well as extracting the dominant macromolecular motions associated with sub-monomer behaviors of i...
International journal of molecular sciences
Jun 18, 2019
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk facto...
Extracting a well-designed energy function is important for protein structure evaluation. Knowledge-based potential functions are one type of the energy functions which can be obtained from known protein structures. The pairwise potential between ato...
Journal of chemical theory and computation
May 14, 2019
In recent years, machine learning (ML) methods have become increasingly popular in computational chemistry. After being trained on appropriate ab initio reference data, these methods allow for accurately predicting the properties of chemical systems,...
The zinc (Zn) cofactor has been proven to be involved in numerous biological mechanisms and the zinc-binding site is recognized as one of the most important post-translation modifications in proteins. Therefore, accurate knowledge of zinc ions in pro...
Flexibility is often a key determinant of protein function. To elucidate the link between their molecular structure and role in an organism, computational techniques such as molecular dynamics can be leveraged to characterize their conformational spa...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 16, 2019
The order of amino acids in a protein sequence enables the protein to acquire a conformation suitable for performing functions, thereby motivating the need to analyze these sequences for predicting functions. Although machine learning based approache...
Journal of chemical information and modeling
Apr 16, 2019
Accurate identification of protein-DNA binding sites is significant for both understanding protein function and drug design. Machine-learning-based methods have been extensively used for the prediction of protein-DNA binding sites. However, the data ...
Proceedings of the National Academy of Sciences of the United States of America
Apr 12, 2019
To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning into the directed evolution workflow. Combinatorial sequ...
Journal of chemical information and modeling
Apr 2, 2019
It has demonstrated that glycogen synthase kinase 3β (GSK3β) is related to Alzheimer's disease (AD). On the basis of the world largest traditional Chinese medicine (TCM) database, a network-pharmacology-based approach was utilized to investigate TCM ...