AIMC Topic: Sequence Analysis, Protein

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DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences.

PLoS computational biology
Identification of drug-target interactions (DTIs) plays a key role in drug discovery. The high cost and labor-intensive nature of in vitro and in vivo experiments have highlighted the importance of in silico-based DTI prediction approaches. In severa...

A novel matrix of sequence descriptors for predicting protein-protein interactions from amino acid sequences.

PloS one
Protein-protein interactions (PPIs) play an important role in the life activities of organisms. With the availability of large amounts of protein sequence data, PPIs prediction methods have attracted increasing attention. A variety of protein sequenc...

End-to-End Differentiable Learning of Protein Structure.

Cell systems
Predicting protein structure from sequence is a central challenge of biochemistry. Co-evolution methods show promise, but an explicit sequence-to-structure map remains elusive. Advances in deep learning that replace complex, human-designed pipelines ...

Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences.

IEEE/ACM transactions on computational biology and bioinformatics
The order of amino acids in a protein sequence enables the protein to acquire a conformation suitable for performing functions, thereby motivating the need to analyze these sequences for predicting functions. Although machine learning based approache...

Seq2seq Fingerprint with Byte-Pair Encoding for Predicting Changes in Protein Stability upon Single Point Mutation.

IEEE/ACM transactions on computational biology and bioinformatics
The engineering of stable proteins is crucial for various industrial purposes. Several machine learning methods have been developed to predict changes in the stability of proteins corresponding to single point mutations. To improve the prediction acc...

NeuroPIpred: a tool to predict, design and scan insect neuropeptides.

Scientific reports
Insect neuropeptides and their associated receptors have been one of the potential targets for the pest control. The present study describes in silico models developed using natural and modified insect neuropeptides for predicting and designing new n...

Classification of Antibacterial Peptides Using Long Short-Term Memory Recurrent Neural Networks.

IEEE/ACM transactions on computational biology and bioinformatics
Antimicrobial peptides are short amino acid sequences that may be antibacterial, antifungal, and antiviral. Most machine learning methodologies applied to identifying antibacterial peptides have developed feature vectors of identical lengths for each...

RPITER: A Hierarchical Deep Learning Framework for ncRNA⁻Protein Interaction Prediction.

International journal of molecular sciences
Non-coding RNAs (ncRNAs) play crucial roles in multiple fundamental biological processes, such as post-transcriptional gene regulation, and are implicated in many complex human diseases. Mostly ncRNAs function by interacting with corresponding RNA-bi...

Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform.

International journal of molecular sciences
It is significant for biological cells to predict self-interacting proteins (SIPs) in the field of bioinformatics. SIPs mean that two or more identical proteins can interact with each other by one gene expression. This plays a major role in the evolu...

SignalP 5.0 improves signal peptide predictions using deep neural networks.

Nature biotechnology
Signal peptides (SPs) are short amino acid sequences in the amino terminus of many newly synthesized proteins that target proteins into, or across, membranes. Bioinformatic tools can predict SPs from amino acid sequences, but most cannot distinguish ...