BACKGROUND: Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein structure prediction, including a ...
Protein Structure Prediction (PSP) is considered to be a complicated problem in computational biology. In spite of, the remarkable progress made by the co-evolution-based method in PSP, it is still a challenging and unresolved problem. Recently, alon...
Protein function is fundamentally reliant on inter-molecular interactions that underpin the ability of proteins to form complexes driving biological processes in living cells. Increasingly, such interactions are recognised as being formed between pro...
Finding optimal parameters for force fields used in molecular simulation is a challenging and time-consuming task, partly due to the difficulty of tuning multiple parameters at once. Automatic differentiation presents a general solution: run a simula...
Journal of chemical information and modeling
Sep 1, 2021
Machine learning scoring functions for protein-ligand binding affinity have been found to consistently outperform classical scoring functions when trained and tested on crystal structures of bound protein-ligand complexes. However, it is less clear h...
The analysis of nuclear magnetic resonance (NMR) spectra for the comprehensive and unambiguous identification and characterization of peaks is a difficult, but critically important step in all NMR analyses of complex biological molecular systems. Her...
The accurate prediction of the relative solvent accessibility of a protein is critical to understanding its 3D structure and biological function. In this study, a novel deep multi-view feature learning (DMVFL) framework that integrates three differen...
Computational chemistry and structure-based design have traditionally been viewed as a subset of tools that could aid acceleration of the drug discovery process, but were not commonly regarded as a driving force in small molecule drug discovery. In t...
Rational protein design aims at the targeted modification of existing proteins. To reach this goal, software suites like Rosetta propose sequences to introduce the desired properties. Challenging design problems necessitate the representation of a pr...
International journal of molecular sciences
Aug 22, 2021
Identifying secretory proteins from blood, saliva or other body fluids has become an effective method of diagnosing diseases. Existing secretory protein prediction methods are mainly based on conventional machine learning algorithms and are highly de...
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