AIMC Topic: Amino Acids

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Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides.

Journal of chemical information and modeling
The discovery of therapeutic peptides is often accelerated by means of virtual screening supported by machine learning-based predictive models. The predictive performance of such models is sensitive to the choice of data and its representation scheme...

iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions.

IEEE/ACM transactions on computational biology and bioinformatics
Among all the PTMs, the protein phosphorylation is pivotal for various pathological and physiological processes. About 30 percent of eukaryotic proteins undergo the phosphorylation modification, leading to various changes in conformation, function, s...

Deep learning study of tyrosine reveals that roaming can lead to photodamage.

Nature chemistry
Amino acids are among the building blocks of life, forming peptides and proteins, and have been carefully 'selected' to prevent harmful reactions caused by light. To prevent photodamage, molecules relax from electronic excited states to the ground st...

Prediction of protein-protein interaction using graph neural networks.

Scientific reports
Proteins are the essential biological macromolecules required to perform nearly all biological processes, and cellular functions. Proteins rarely carry out their tasks in isolation but interact with other proteins (known as protein-protein interactio...

A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model.

BMC bioinformatics
BACKGROUND: Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cultural value. Studies have sh...

Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin.

PeerJ
Alkaline soil is widely distributed in China. Its rational utilization is an effective measure to solve land shortage and improve the environment. Alfalfa is characterized by strong salt and alkali tolerance and high yield and protein content. Nitrog...

XGB-DrugPred: computational prediction of druggable proteins using eXtreme gradient boosting and optimized features set.

Scientific reports
Accurate identification of drug-targets in human body has great significance for designing novel drugs. Compared with traditional experimental methods, prediction of drug-targets via machine learning algorithms has enhanced the attention of many rese...

Hierarchical representation for PPI sites prediction.

BMC bioinformatics
BACKGROUND: Protein-protein interactions have pivotal roles in life processes, and aberrant interactions are associated with various disorders. Interaction site identification is key for understanding disease mechanisms and design new drugs. Effectiv...

Large-scale design and refinement of stable proteins using sequence-only models.

PloS one
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be ...

Accurate positioning of functional residues with robotics-inspired computational protein design.

Proceedings of the National Academy of Sciences of the United States of America
SignificanceComputational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level geom...