AIMC Topic: Proteins

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Combining sequence and Gene Ontology for protein module detection in the Weighted Network.

Journal of theoretical biology Oct 29, 2016
Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating ...
Sequence Analysis, Protein Proteins Gene Ontology
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Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids.

International journal of molecular sciences Oct 26, 2016
Information about the interface sites of Protein-Protein Interactions (PPIs) is useful for many biological research works. However, despite the advancement of experimental techniques, the identification of PPI sites still remains as a challenging tas...
Humans Machine Learning Protein Interaction Domains and Motifs Amino Acids Models, Biological Intrinsically Disordered Proteins Protein Interaction Mapping Proteins Databases, Protein Animals Protein Interaction Maps
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Machine Learning Approaches for Predicting Protein Complex Similarity.

Journal of computational biology : a journal of computational molecular cell biology Oct 17, 2016
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interac...
Neural Networks, Computer Machine Learning Protein Binding Animals Humans Proteins Molecular Docking Simulation Protein Conformation
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Detecting Essential Proteins Based on Network Topology, Gene Expression Data, and Gene Ontology Information.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2016
The identification of essential proteins in protein-protein interaction (PPI) networks is of great significance for understanding cellular processes. With the increasing availability of large-scale PPI data, numerous centrality measures based on netw...
Gene Ontology Protein Interaction Mapping Yeasts Molecular Sequence Annotation Transcriptome Proteins Databases, Protein
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Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines.

Journal of chemical information and modeling Sep 22, 2016
Carbohydrate-binding proteins play significant roles in many diseases including cancer. Here, we established a machine-learning-based method (called sequence-based prediction of residue-level interaction sites of carbohydrates, SPRINT-CBH) to predict...
Protein Binding Support Vector Machine Proteins Databases, Protein Molecular Docking Simulation ROC Curve Carbohydrate Metabolism Carbohydrates Binding Sites Humans
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Reduction strategies for hierarchical multi-label classification in protein function prediction.

BMC bioinformatics Sep 15, 2016
BACKGROUND: Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the hierarchy. This scenario is t...
Proteins Neural Networks, Computer
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Predicting protein subcellular localization based on information content of gene ontology terms.

Computational biology and chemistry Sep 14, 2016
Predicting the location where a protein resides within a cell is important in cell biology. Computational approaches to this issue have attracted more and more attentions from the community of biomedicine. Among the protein features used to predict t...
Proteins Databases, Protein Subcellular Fractions Gene Ontology Support Vector Machine
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Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach.

BMC bioinformatics Sep 13, 2016
BACKGROUND: Protein secondary structure prediction (SSP) has been an area of intense research interest. Despite advances in recent methods conducted on large datasets, the estimated upper limit accuracy is yet to be reached. Since the predictions of ...
Protein Structure, Secondary Neural Networks, Computer Proteins Humans
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A D3R prospective evaluation of machine learning for protein-ligand scoring.

Journal of computer-aided molecular design Sep 3, 2016
We assess the performance of several machine learning-based scoring methods at protein-ligand pose prediction, virtual screening, and binding affinity prediction. The methods and the manner in which they were trained make them sufficiently diverse to...
HSP90 Heat-Shock Proteins Molecular Docking Simulation Protein Binding Algorithms Ligands Prospective Studies Humans Computational Biology Binding Sites Machine Learning Proteins
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Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning.

IEEE/ACM transactions on computational biology and bioinformatics Aug 24, 2016
The function of a protein is determined by its structure, which creates a need for efficient methods of protein structure determination to advance scientific and medical research. Because current experimental structure determination methods carry a h...
Computational Biology Machine Learning Proteins Support Vector Machine Algorithms Databases, Protein
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