AIMC Topic: Amino Acid Sequence

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Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features.

BMC bioinformatics Dec 23, 2016
BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune deficiency syndrome (AIDS). Dev...
Amino Acid Sequence HIV-1 Data Accuracy Substrate Specificity HIV Protease Humans Neural Networks, Computer Protein Conformation Algorithms HIV Infections Computational Biology Decision Trees
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Mapping membrane activity in undiscovered peptide sequence space using machine learning.

Proceedings of the National Academy of Sciences of the United States of America Nov 14, 2016
There are some ∼1,100 known antimicrobial peptides (AMPs), which permeabilize microbial membranes but have diverse sequences. Here, we develop a support vector machine (SVM)-based classifier to investigate ⍺-helical AMPs and the interrelated nature o...
Anti-Bacterial Agents Anti-Infective Agents Peptides Machine Learning Antimicrobial Cationic Peptides Amino Acid Sequence Cell Membrane X-Ray Diffraction Microbial Sensitivity Tests Models, Theoretical Support Vector Machine
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Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs.

IEEE/ACM transactions on computational biology and bioinformatics Oct 11, 2016
Protein-DNA interactions are ubiquitous in a wide variety of biological processes. Correctly locating DNA-binding residues solely from protein sequences is an important but challenging task for protein function annotations and drug discovery, especia...
DNA-Binding Proteins Amino Acid Sequence Models, Statistical Computational Biology Databases, Protein Support Vector Machine
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SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity.

PloS one Aug 15, 2016
Knowledge of protein function is important for biological, medical and therapeutic studies, but many proteins are still unknown in function. There is a need for more improved functional prediction methods. Our SVM-Prot web-server employed a machine l...
Internet Amino Acid Sequence Sequence Alignment Support Vector Machine Computational Biology Proteins Databases, Protein
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Machine Learning of Protein Interactions in Fungal Secretory Pathways.

PloS one Jul 21, 2016
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict prote...
Protein Interaction Mapping Genome, Fungal Secretory Pathway Fungal Proteins Saccharomyces cerevisiae Trichoderma Protein Interaction Maps Machine Learning Databases, Protein Evolution, Molecular Algorithms Amino Acid Sequence ROC Curve
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gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.

Journal of theoretical biology Jul 1, 2016
DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which ...
ROC Curve Computational Biology Support Vector Machine Amino Acid Sequence Models, Molecular Databases, Protein Genome Protein Domains Principal Component Analysis Numerical Analysis, Computer-Assisted DNA-Binding Proteins DNA
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GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

Proteins Jun 8, 2016
G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Area Under Curve Models, Molecular Amino Acid Sequence Support Vector Machine Databases, Protein Receptors, G-Protein-Coupled Protein Interaction Domains and Motifs Binding Sites Protein Structure, Secondary Protein Multimerization Humans Protein Binding Mice Animals ROC Curve
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A Web Server and Mobile App for Computing Hemolytic Potency of Peptides.

Scientific reports Mar 8, 2016
Numerous therapeutic peptides do not enter the clinical trials just because of their high hemolytic activity. Recently, we developed a database, Hemolytik, for maintaining experimentally validated hemolytic and non-hemolytic peptides. The present stu...
Sequence Analysis, Protein Hemolytic Agents Computer Simulation Internet Peptides Amino Acid Sequence Mobile Applications Hemolysis Humans Support Vector Machine Databases, Protein
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UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.

Bioinformatics (Oxford, England) Mar 7, 2016
MOTIVATION: Similarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation. New approaches that overcome the limitations of methods that rely solely upon sequ...
Databases, Protein Amino Acid Sequence Knowledge Bases Molecular Sequence Annotation Proteins
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Predicting lysine phosphoglycerylation with fuzzy SVM by incorporating k-spaced amino acid pairs into Chou׳s general PseAAC.

Journal of theoretical biology Feb 22, 2016
As a new type of post-translational modification, lysine phosphoglycerylation plays a key role in regulating glycolytic process and metabolism in cells. Due to the traditional experimental methods are time-consuming and labor-intensive, it is importa...
Software Algorithms Reproducibility of Results Fuzzy Logic Protein Processing, Post-Translational Computational Biology Support Vector Machine Binding Sites Diphosphoglyceric Acids Amino Acids Amino Acid Sequence Lysine
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