Computational and mathematical methods in medicine
Mar 28, 2020
Prediction of DNA-binding proteins (DBPs) has become a popular research topic in protein science due to its crucial role in all aspects of biological activities. Even though considerable efforts have been devoted to developing powerful computational ...
As an important category of proteins, alpha-helix transmembrane proteins (TMPs) play an important role in various biological activities. Because the solved αTMP structures are inadequate, predicting the residue contacts among the transmembrane segmen...
Journal of computer-aided molecular design
Mar 17, 2020
Scoring functions are routinely deployed in structure-based drug design to quantify the potential for protein-ligand (PL) complex formation. Here, we present a new scoring function Bappl+ that is designed to predict the binding affinities of non-meta...
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...
Drug-Target interaction (DTI) plays a crucial role in drug discovery, drug repositioning and understanding the drug side effects which helps to identify new therapeutic profiles for various diseases. However, the exponential growth in the genomic and...
Data on experimentally-characterized animal mitochondrial proteomes (mt-proteomes) are limited to a few model organisms and are scattered across multiple databases, impeding a comparative analysis. We developed two resources to address these problems...
Discovery and development of biopeptides are time-consuming, laborious, and dependent on various factors. Data-driven computational methods, especially machine learning (ML) approach, can rapidly and efficiently predict the utility of therapeutic pep...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 10, 2020
Protein-Protein Interactions (PPIs) play an irreplaceable role in biological activities of organisms. Although many high-throughput methods are used to identify PPIs from different kinds of organisms, they have some shortcomings, such as high cost an...
Data-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of samples. However, sample-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA ...
Designing protein sequences that fold to a given three-dimensional (3D) structure has long been a challenging problem in computational structural biology with significant theoretical and practical implications. In this study, we first formulated this...