AIMC Topic: Sequence Analysis, Protein

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TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning.

IEEE/ACM transactions on computational biology and bioinformatics
Accurately identifying DNA-binding proteins (DBPs) from protein sequence information is an important but challenging task for protein function annotations. In this paper, we establish a novel computational method, named TargetDBP, for accurately targ...

DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure.

PloS one
Rapid, accurate prediction of protein structure from amino acid sequence would accelerate fields as diverse as drug discovery, synthetic biology and disease diagnosis. Massively improved prediction of protein structures has been driven by improving t...

Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning.

Scientific reports
RNA binding protein (RBP) plays an important role in cellular processes. Identifying RBPs by computation and experiment are both essential. Recently, an RBP predictor, RBPPred, is proposed in our group to predict RBPs. However, RBPPred is too slow fo...

Decision-Tree Based Meta-Strategy Improved Accuracy of Disorder Prediction and Identified Novel Disordered Residues Inside Binding Motifs.

International journal of molecular sciences
Using computational techniques to identify intrinsically disordered residues is practical and effective in biological studies. Therefore, designing novel high-accuracy strategies is always preferable when existing strategies have a lot of room for im...

Predicting improved protein conformations with a temporal deep recurrent neural network.

PloS one
Accurate protein structure prediction from amino acid sequence is still an unsolved problem. The most reliable methods centre on template based modelling. However, the accuracy of these models entirely depends on the availability of experimentally re...

BlaPred: Predicting and classifying β-lactamase using a 3-tier prediction system via Chou's general PseAAC.

Journal of theoretical biology
Antibiotics of β-lactam class account for nearly half of the global antibiotic use. The β-lactamase enzyme is a major element of the bacterial arsenals to escape the lethal effect of β-lactam antibiotics. Different variants of β-lactamases have evolv...

KELM-CPPpred: Kernel Extreme Learning Machine Based Prediction Model for Cell-Penetrating Peptides.

Journal of proteome research
Cell-penetrating peptides (CPPs) facilitate the transport of pharmacologically active molecules, such as plasmid DNA, short interfering RNA, nanoparticles, and small peptides. The accurate identification of new and unique CPPs is the initial step to ...

Predicting membrane protein types by incorporating a novel feature set into Chou's general PseAAC.

Journal of theoretical biology
Membrane proteins are vital type of proteins that serve as channels, receptors and energy transducers in a cell. They perform various important functions, which are mainly associated with their types. They are also attractive targets of drug discover...

PROSES: A Web Server for Sequence-Based Protein Encoding.

Journal of computational biology : a journal of computational molecular cell biology
Recently, the number of the amino acid sequences shared in online databases is growing rapidly in huge amounts. By using sequence-derived features, machine learning algorithms are successfully applied to prediction of protein functional classes, prot...

RFAmyloid: A Web Server for Predicting Amyloid Proteins.

International journal of molecular sciences
Amyloid is an insoluble fibrous protein and its mis-aggregation can lead to some diseases, such as Alzheimer's disease and Creutzfeldt⁻Jakob's disease. Therefore, the identification of amyloid is essential for the discovery and understanding of disea...