AIMC Topic: Position-Specific Scoring Matrices

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CrystalM: A Multi-View Fusion Approach for Protein Crystallization Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Feb 3, 2021
Improving the accuracy of predicting protein crystallization is very important for protein crystallization projects, which is a critical step for the determination of protein structure by X-ray crystallography. At present, many machine learning metho...
Computational Biology Crystallization Sequence Analysis, Protein Position-Specific Scoring Matrices Models, Statistical Proteins Support Vector Machine
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TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features.

Journal of chemical information and modeling Jan 7, 2021
Protein-DNA interactions exist ubiquitously and play important roles in the life cycles of living cells. The accurate identification of DNA-binding proteins (DBPs) is one of the key steps to understand the mechanisms of protein-DNA interactions. Alth...
Binding Sites Position-Specific Scoring Matrices Databases, Protein DNA-Binding Proteins Algorithms Support Vector Machine
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iT3SE-PX: Identification of Bacterial Type III Secreted Effectors Using PSSM Profiles and XGBoost Feature Selection.

Computational and mathematical methods in medicine Jan 6, 2021
Identification of bacterial type III secreted effectors (T3SEs) has become a popular research topic in the field of bioinformatics due to its crucial role in understanding host-pathogen interaction and developing better therapeutic targets against th...
Amino Acid Sequence Position-Specific Scoring Matrices Type III Secretion Systems Computational Biology Support Vector Machine Machine Learning Databases, Protein Algorithms
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Computational Identification and Analysis of Ubiquinone-Binding Proteins.

Cells Feb 24, 2020
Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will...
Carrier Proteins Amino Acid Sequence Ubiquinone Computational Biology Membrane Proteins Sequence Analysis, Protein Protein Interaction Domains and Motifs Position-Specific Scoring Matrices Gene Ontology Binding Sites Machine Learning Protein Binding Humans
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iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks.

BMC bioinformatics Dec 27, 2019
BACKGROUND: Since protein-DNA interactions are highly essential to diverse biological events, accurately positioning the location of the DNA-binding residues is necessary. This biological issue, however, is currently a challenging task in the age of ...
Position-Specific Scoring Matrices DNA-Binding Proteins Amino Acid Sequence Algorithms Reproducibility of Results DNA Humans ROC Curve Software Amino Acids Neural Networks, Computer
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Classification of adaptor proteins using recurrent neural networks and PSSM profiles.

BMC genomics Dec 24, 2019
BACKGROUND: Adaptor proteins are carrier proteins that play a crucial role in signal transduction. They commonly consist of several modular domains, each having its own binding activity and operating by forming complexes with other intracellular-sign...
Adaptor Proteins, Signal Transducing Position-Specific Scoring Matrices Deep Learning ROC Curve
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Efficient utilization on PSSM combining with recurrent neural network for membrane protein types prediction.

Computational biology and chemistry Aug 8, 2019
Position-Specific Scoring Matrix (PSSM) is an excellent feature extraction method that was proposed early in protein classifying prediction, but within the restriction of feature shape in PSSM, researchers make a lot attempts to process it so that PS...
Neural Networks, Computer Computational Biology Position-Specific Scoring Matrices Membrane Proteins Databases, Protein
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An Ensemble Classifier to Predict Protein-Protein Interactions by Combining PSSM-based Evolutionary Information with Local Binary Pattern Model.

International journal of molecular sciences Jul 17, 2019
Protein plays a critical role in the regulation of biological cell functions. Among them, whether proteins interact with each other has become a fundamental problem, because proteins usually perform their functions by interacting with other proteins....
Protein Interaction Mapping Position-Specific Scoring Matrices Computational Biology Humans Support Vector Machine Software Databases, Protein
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Prediction of ATP-binding sites in membrane proteins using a two-dimensional convolutional neural network.

Journal of molecular graphics & modelling Jul 15, 2019
Membrane proteins, the most important drug targets, account for around 30% of total proteins encoded by the genome of living organisms. An important role of these proteins is to bind adenosine triphosphate (ATP), facilitating crucial biological proce...
Amino Acid Motifs Web Browser Position-Specific Scoring Matrices Computational Biology Adenosine Triphosphate Algorithms Binding Sites Neural Networks, Computer Membrane Proteins Reproducibility of Results Machine Learning Models, Theoretical ROC Curve Databases, Protein Amino Acid Sequence
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ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins.

BMC bioinformatics Jul 6, 2019
BACKGROUND: Electron transport chain is a series of protein complexes embedded in the process of cellular respiration, which is an important process to transfer electrons and other macromolecules throughout the cell. It is also the major process to e...
Electron Transport Position-Specific Scoring Matrices Electron Transport Chain Complex Proteins Humans Neural Networks, Computer Software
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