AIMC Topic: Position-Specific Scoring Matrices

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Deep-GB: A novel deep learning model for globular protein prediction using CNN-BiLSTM architecture and enhanced PSSM with trisection strategy.

IET systems biology Nov 8, 2024
Globular proteins (GPs) play vital roles in a wide range of biological processes, encompassing enzymatic catalysis and immune responses. Enzymes, among these globular proteins, facilitate biochemical reactions, while others, such as haemoglobin, cont...
Neural Networks, Computer Deep Learning Databases, Protein Position-Specific Scoring Matrices Computational Biology Proteins
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PSSM-Sumo: deep learning based intelligent model for prediction of sumoylation sites using discriminative features.

BMC bioinformatics Aug 30, 2024
Post-translational modifications (PTMs) are fundamental to essential biological processes, exerting significant influence over gene expression, protein localization, stability, and genome replication. Sumoylation, a PTM involving the covalent additio...
Humans Computational Biology Support Vector Machine Algorithms Deep Learning Position-Specific Scoring Matrices Protein Processing, Post-Translational Sumoylation
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StackDPPred: Multiclass prediction of defensin peptides using stacked ensemble learning with optimized features.

Methods (San Diego, Calif.) Aug 22, 2024
Host defense or antimicrobial peptides (AMPs) are promising candidates for protecting host against microbial pathogens for example bacteria, virus, fungi, yeast. Defensins are the type of AMPs that act as potential therapeutic drug agent and perform ...
Amino Acid Sequence Position-Specific Scoring Matrices Algorithms Computational Biology Principal Component Analysis Defensins Machine Learning
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Hybrid framework for membrane protein type prediction based on the PSSM.

Scientific reports Jul 26, 2024
Membrane proteins are considered the major source of drug targets and are indispensable for drug design and disease prevention. However, traditional biomechanical experiments are costly and time-consuming; thus, many computational methods for predict...
Position-Specific Scoring Matrices Membrane Proteins Databases, Protein Machine Learning Algorithms Deep Learning Computational Biology Humans Neural Networks, Computer
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Machine learning-based model for accurate identification of druggable proteins using light extreme gradient boosting.

Journal of biomolecular structure & dynamics Oct 18, 2023
The identification of druggable proteins (DPs) is significant for the development of new drugs, personalized medicine, understanding of disease mechanisms, drug repurposing, and economic benefits. By identifying new druggable targets, researchers can...
Amino Acids Position-Specific Scoring Matrices Algorithms Humans Drug Discovery Machine Learning Computational Biology Proteins
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plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style.

BMC genomics Oct 3, 2023
BACKGROUND: The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learnin...
Artificial Intelligence Software Computational Biology Programming Languages Position-Specific Scoring Matrices
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Deep-AGP: Prediction of angiogenic protein by integrating two-dimensional convolutional neural network with discrete cosine transform.

International journal of biological macromolecules Jun 8, 2023
Angiogenic proteins (AGPs) play a primary role in the formation of new blood vessels from pre-existing ones. AGPs have diverse applications in cancer, including serving as biomarkers, guiding anti-angiogenic therapies, and aiding in tumor imaging. Un...
Position-Specific Scoring Matrices Neural Networks, Computer Machine Learning
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Identification of adaptor proteins by incorporating deep learning and PSSM profiles.

Methods (San Diego, Calif.) Nov 22, 2022
Adaptor proteins, also known as signal transduction adaptor proteins, are important proteins in signal transduction pathways, and play a role in connecting signal proteins for signal transduction between cells. Studies have shown that adaptor protein...
Adaptor Proteins, Signal Transducing Position-Specific Scoring Matrices Algorithms Neural Networks, Computer Deep Learning Software
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Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles.

Journal of chemical information and modeling Sep 27, 2022
: SNARE proteins play a vital role in membrane fusion and cellular physiology and pathological processes. Many potential therapeutics for mental diseases or even cancer based on SNAREs are also developed. Therefore, there is a dire need to predict th...
Position-Specific Scoring Matrices SNARE Proteins Neural Networks, Computer
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IDRBP-PPCT: Identifying Nucleic Acid-Binding Proteins Based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two important nucleic acid-binding proteins (NABPs), which play important roles in biological processes such as replication, translation and transcription of genetic material. Some prote...
Position-Specific Scoring Matrices Databases, Protein RNA-Binding Proteins DNA-Binding Proteins Algorithms DNA Support Vector Machine Amino Acid Sequence Computational Biology
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