AIMC Topic: Protein Interaction Mapping

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Application of Machine Learning Approaches for Protein-protein Interactions Prediction.

Medicinal chemistry (Shariqah (United Arab Emirates)) Jan 1, 2017
BACKGROUND: Proteomics endeavors to study the structures, functions and interactions of proteins. Information of the protein-protein interactions (PPIs) helps to improve our knowledge of the functions and the 3D structures of proteins. Thus determini...
Computational Biology Humans Protein Interaction Mapping Machine Learning Animals
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Computational Methods to Predict Protein Functions from Protein-Protein Interaction Networks.

Current protein & peptide science Jan 1, 2017
Predicting functions of proteins is a key issue in the post-genomic era. Some experimental methods have been designed to predict protein functions. However, these methods cannot accommodate the vast amount of sequence data due to their inherent diffi...
Neural Networks, Computer Machine Learning Computational Biology Humans Proteins Protein Interaction Mapping Support Vector Machine Decision Trees
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An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2017
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to ...
Protein Binding Computational Biology Signal Transduction Databases, Protein Phosphotyrosine Humans Web Browser Workflow Algorithms Protein Interaction Domains and Motifs Reproducibility of Results Supervised Machine Learning src Homology Domains Protein Interaction Mapping
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Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix.

Oncotarget Dec 13, 2016
Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interact...
Humans Computational Biology Fungal Proteins Protein Interaction Mapping Sequence Analysis, Protein Position-Specific Scoring Matrices Support Vector Machine Databases, Protein Principal Component Analysis
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Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods.

Molecular bioSystems Mar 1, 2016
Protein-protein interactions (PPIs) play a vital role in most biological processes. Hence their comprehension can promote a better understanding of the mechanisms underlying living systems. However, besides the cost and the time limitation involved i...
Probability Protein Interaction Mapping Computational Biology Databases, Protein Sample Size ROC Curve Protein Binding Machine Learning Reproducibility of Results
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A systematic approach to prioritize drug targets using machine learning, a molecular descriptor-based classification model, and high-throughput screening of plant derived molecules: a case study in oral cancer.

Molecular bioSystems Dec 1, 2015
Systems-biology inspired identification of drug targets and machine learning-based screening of small molecules which modulate their activity have the potential to revolutionize modern drug discovery by complementing conventional methods. To utilize ...
Molecular Conformation Binding Sites Protein Interaction Mapping Models, Molecular Mouth Neoplasms High-Throughput Screening Assays Machine Learning Gene Expression Regulation, Neoplastic Drug Discovery Antineoplastic Agents, Phytogenic Cell Line, Tumor Receptors, CXCR4 Protein Binding Computational Biology ROC Curve Gene Regulatory Networks Humans
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Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

Journal of biosciences Oct 1, 2015
Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown tha...
Protein Interaction Mapping Protein Interaction Domains and Motifs Area Under Curve Gene Expression Escherichia coli Proteins Support Vector Machine Escherichia coli Fuzzy Logic Databases, Protein Humans Sensitivity and Specificity
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Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer.

IET systems biology Aug 1, 2015
Constructing interaction network from biomedical texts is a very important and interesting work. The authors take advantage of text mining and reinforcement learning approaches to establish protein interaction network. Considering the high computatio...
Prostatic Neoplasms Periodicals as Topic Signal Transduction PubMed Data Mining Neoplasm Proteins Humans Protein Interaction Mapping Natural Language Processing Machine Learning Male
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Predicting Protein-Protein Interaction Sites with a Novel Membership Based Fuzzy SVM Classifier.

IEEE/ACM transactions on computational biology and bioinformatics Jan 1, 2015
Predicting residues that participate in protein-protein interactions (PPI) helps to identify, which amino acids are located at the interface. In this paper, we show that the performance of the classical support vector machine (SVM) algorithm can furt...
Pattern Recognition, Automated Molecular Sequence Data Sequence Analysis, Protein Sequence Alignment Binding Sites Protein Interaction Mapping Algorithms Humans Computer Simulation Protein Binding Fuzzy Logic Models, Statistical Models, Chemical Amino Acid Sequence
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Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data.

IEEE/ACM transactions on computational biology and bioinformatics Jan 1, 2015
Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to...
Humans Animals Protein Interaction Mapping Gene Expression Profiling Proteome Signal Transduction Kinetics Models, Biological Fuzzy Logic Models, Statistical
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