AIMC Topic: Amino Acid Sequence

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Accurate contact predictions using covariation techniques and machine learning.

Proteins Aug 14, 2015
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Computational Biology Models, Statistical Proteins Databases, Protein Software Computer Simulation Bacteria Protein Structure, Secondary Protein Folding Sequence Alignment Protein Interaction Domains and Motifs Models, Molecular Humans Internet Neural Networks, Computer Amino Acid Sequence Machine Learning Viruses
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Prediction of Peptide and Protein Propensity for Amyloid Formation.

PloS one Aug 4, 2015
Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo str...
Protein Structure, Secondary Neural Networks, Computer Amyloidogenic Proteins Amino Acid Sequence Amyloid
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High-order neural networks and kernel methods for peptide-MHC binding prediction.

Bioinformatics (Oxford, England) Jul 23, 2015
MOTIVATION: Effective computational methods for peptide-protein binding prediction can greatly help clinical peptide vaccine search and design. However, previous computational methods fail to capture key nonlinear high-order dependencies between diff...
Major Histocompatibility Complex Protein Binding Support Vector Machine Databases, Protein Area Under Curve Epitopes Amino Acid Sequence Molecular Sequence Data Neural Networks, Computer Algorithms Peptides Humans ROC Curve
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Identification of Heat Shock Protein families and J-protein types by incorporating Dipeptide Composition into Chou's general PseAAC.

Computer methods and programs in biomedicine Jul 22, 2015
Heat Shock Proteins (HSPs) are the substantial ingredients for cell growth and viability, which are found in all living organisms. HSPs manage the process of folding and unfolding of proteins, the quality of newly synthesized proteins and protecting ...
Sequence Alignment Sequence Analysis, Protein Reproducibility of Results Sensitivity and Specificity Machine Learning Dipeptides Amino Acid Sequence Algorithms Pattern Recognition, Automated Heat-Shock Proteins Molecular Sequence Data HSP70 Heat-Shock Proteins
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PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides.

BMC bioinformatics Jul 5, 2015
BACKGROUND: Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successful group of these peptides in...
Amino Acid Sequence Disulfides Molecular Sequence Data Cystine Animals Algorithms Support Vector Machine Models, Statistical Peptide Fragments
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A novel method based on physicochemical properties of amino acids and one class classification algorithm for disease gene identification.

Journal of biomedical informatics Jul 2, 2015
Identifying the genes that cause disease is one of the most challenging issues to establish the diagnosis and treatment quickly. Several interesting methods have been introduced for disease gene identification for a decade. In general, the main diffe...
Algorithms Reproducibility of Results Diagnosis, Computer-Assisted ROC Curve Humans Artificial Intelligence Proteins Principal Component Analysis Amino Acids Amino Acid Sequence Computational Biology Support Vector Machine Parkinson Disease Regression Analysis Probability False Positive Reactions
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TRAL: tandem repeat annotation library.

Bioinformatics (Oxford, England) May 18, 2015
MOTIVATION: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.
Software Cluster Analysis Databases, Protein Amino Acid Sequence Gene Library Humans Knowledge Bases Molecular Sequence Data Documentation Tandem Repeat Sequences Molecular Sequence Annotation
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Machine learning applications in genetics and genomics.

Nature reviews. Genetics May 7, 2015
The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets. Here, we provide an overview of machine learning ap...
Base Sequence Genetics, Medical Molecular Sequence Annotation Genomics Models, Genetic Discriminant Analysis Amino Acid Sequence Artificial Intelligence Computer Simulation Animals Humans
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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.

Nature methods May 4, 2015
Protein phosphorylation is important in cellular pathways and altered in disease. We developed MIMP (http://mimp.baderlab.org/), a machine learning method to predict the impact of missense single-nucleotide variants (SNVs) on kinase-substrate interac...
Artificial Intelligence Software Polymorphism, Single Nucleotide Signal Transduction Mutation, Missense Phosphorylation Phosphotransferases Amino Acid Sequence Substrate Specificity
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Machine learning assisted design of highly active peptides for drug discovery.

PLoS computational biology Apr 7, 2015
The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning ap...
Drug Discovery Molecular Sequence Data Amino Acid Sequence Machine Learning Antimicrobial Cationic Peptides Sequence Analysis, Protein Pattern Recognition, Automated Peptides Structure-Activity Relationship Bacterial Physiological Phenomena Protein Interaction Mapping
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