In this paper, a step-by-step classification algorithm based on double-layer SVM model is constructed to predict the secondary structure of proteins. The most important feature of this algorithm is to improve the prediction accuracy of α+β and α/β cl...
Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative for su...
Accurate prediction of protein secondary structure (alpha-helix, beta-strand and coil) is a crucial step for protein inter-residue contact prediction and ab initio tertiary structure prediction. In a previous study, we developed a deep belief network...
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...
FASEB journal : official publication of the Federation of American Societies for Experimental Biology
33368572
β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery...
Protein structure prediction is a long-standing unsolved problem in molecular biology that has seen renewed interest with the recent success of deep learning with AlphaFold at CASP13. While developing and evaluating protein structure prediction metho...
Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
33656309
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...
In the process of drug discovery, identifying the interaction between the protein and the novel compound plays an important role. With the development of technology, deep learning methods have shown excellent performance in various situations. Howeve...
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we show that, although these deep learning approaches have originally been develop...