AIMC Topic: Position-Specific Scoring Matrices

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SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification.

Computational biology and chemistry Apr 6, 2022
Membrane protein classification is a key to inferring the function of uncharacterized membrane protein. To get around the time-consuming and expensive biochemical experiments in the wet lab, there has been a lot of research focusing on developing fas...
Attention Position-Specific Scoring Matrices Deep Learning Membrane Proteins Neural Networks, Computer
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MFPS_CNN: Multi-filter Pattern Scanning from Position-specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters.

Molecular informatics Apr 5, 2022
In cellular transportation mechanisms, the movement of ions across the cell membrane and its proper control are important for cells, especially for life processes. Ion transporters/pumps and ion channel proteins work as border guards controlling the ...
Membrane Proteins Ions Position-Specific Scoring Matrices Neural Networks, Computer Algorithms
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DeepDNAbP: A deep learning-based hybrid approach to improve the identification of deoxyribonucleic acid-binding proteins.

Computers in biology and medicine Mar 30, 2022
Accurate identification of DNA-binding proteins (DBPs) is critical for both understanding protein function and drug design. DBPs also play essential roles in different kinds of biological activities such as DNA replication, repair, transcription, and...
DNA DNA-Binding Proteins Deep Learning Position-Specific Scoring Matrices Neural Networks, Computer Computational Biology
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Prediction of FMN Binding Sites in Electron Transport Chains Based on 2-D CNN and PSSM Profiles.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2021
Flavin mono-nucleotides (FMNs) are cofactors that hold responsibility for carrying and transferring electrons in the electron transport chain stage of cellular respiration. Without being facilitated by FMNs, energy production is stagnant due to the i...
Algorithms Deep Learning Neural Networks, Computer Electron Transport Position-Specific Scoring Matrices Computational Biology Binding Sites Flavin Mononucleotide
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Predicting subcellular location of protein with evolution information and sequence-based deep learning.

BMC bioinformatics Oct 22, 2021
BACKGROUND: Protein subcellular localization prediction plays an important role in biology research. Since traditional methods are laborious and time-consuming, many machine learning-based prediction methods have been proposed. However, most of the p...
Position-Specific Scoring Matrices Computational Biology Proteins Databases, Protein Amino Acid Sequence Deep Learning
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DBP-GAPred: An intelligent method for prediction of DNA-binding proteins types by enhanced evolutionary profile features with ensemble learning.

Journal of bioinformatics and computational biology Jul 21, 2021
DNA-binding proteins (DBPs) perform an influential role in diverse biological activities like DNA replication, slicing, repair, and transcription. Some DBPs are indispensable for understanding many types of human cancers (i.e. lung, breast, and liver...
Position-Specific Scoring Matrices DNA-Binding Proteins Amino Acid Sequence Algorithms Computational Biology Support Vector Machine Humans Databases, Protein
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MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics.

BMC bioinformatics May 7, 2021
BACKGROUND: Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are enriched in specific sequence mot...
Algorithms Support Vector Machine Position-Specific Scoring Matrices Base Sequence Nucleotide Motifs
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An Ensemble Learning-Based Method for Inferring Drug-Target Interactions Combining Protein Sequences and Drug Fingerprints.

BioMed research international Apr 24, 2021
Identifying the interactions of the drug-target is central to the cognate areas including drug discovery and drug reposition. Although the high-throughput biotechnologies have made tremendous progress, the indispensable clinical trials remain to be e...
Databases, Protein Computational Biology Machine Learning Drug Interactions Support Vector Machine Drug Discovery Amino Acid Sequence Position-Specific Scoring Matrices
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Disentangling the Contribution of Each Descriptive Characteristic of Every Single Mutation to Its Functional Effects.

Journal of chemical information and modeling Mar 23, 2021
Mutational effects predictions continue to improve in accuracy as advanced artificial intelligence (AI) algorithms are trained on exhaustive experimental data. The next natural questions to ask are if it is possible to gain insights into which attrib...
Mutation Position-Specific Scoring Matrices Algorithms Proteins Artificial Intelligence
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Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning.

Journal of computational biology : a journal of computational molecular cell biology Feb 22, 2021
Position-Specific Scoring Matrices Deep Learning Computational Biology Neural Networks, Computer Proteins Algorithms Protein Structure, Secondary Protein Conformation Sequence Alignment
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