Computational and mathematical methods in medicine
May 31, 2021
Diabetic retinopathy occurs as a result of the harmful effects of diabetes on the eyes. Diabetic retinopathy is also a disease that should be diagnosed early. If not treated early, vision loss may occur. It is estimated that one third of more than ha...
As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) plays a crucial role in controlling gene replication, expression, cell cycle, DNA replication, and differentiation. The accurate identification of 4mC sites is necessary to und...
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main challenges in computational biology and chemistry. Predicting any protein's accurate structure is of paramount importance for the scientific community, as the...
International journal of molecular sciences
May 28, 2021
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and th...
The design of CRISPR gRNAs requires accurate on-target efficiency predictions, which demand high-quality gRNA activity data and efficient modeling. To advance, we here report on the generation of on-target gRNA activity data for 10,592 SpCas9 gRNAs. ...
BACKGROUND: Direct link between metabolism and cell and organism phenotype in health and disease makes metabolomics, a high throughput study of small molecular metabolites, an essential methodology for understanding and diagnosing disease development...
Lysine succinylation is a typical protein post-translational modification and plays a crucial role of regulation in the cellular process. Identifying succinylation sites is fundamental to explore its functions. Although many computational methods wer...
The rapid increase in the number of proteins in sequence databases and the diversity of their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network for predicting pro...
The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To further leverage the improved inter-resid...
Searching for possible biochemical networks that perform a certain function is a challenge in systems biology. For simple functions and small networks, this can be achieved through an exhaustive search of the network topology space. However, it is di...
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