AIMC Topic: Amino Acid Sequence

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CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes.

BMC bioinformatics Dec 28, 2017
BACKGROUND: The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperative to develop a computationa...
Models, Molecular Neural Networks, Computer Amino Acid Sequence beta-Lactamases ROC Curve Databases, Protein Algorithms Reproducibility of Results
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Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction.

BMC bioinformatics Dec 28, 2017
BACKGROUND: Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being actively developed. Recently, m...
Internet Alleles Histocompatibility Antigens Class I Amino Acid Sequence Peptides Deep Learning Protein Binding Machine Learning Reproducibility of Results Animals Humans
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Design and synthesis of cell selective α/β-diastereomeric peptidomimetic with potent in vivo antibacterial activity against methicillin resistant S. Aureus.

Bioorganic chemistry Dec 26, 2017
Design of therapeutically viable antimicrobial peptides with cell selectivity against microorganisms is an important step towards the development of new antimicrobial agents. Here, we report four de novo designed, short amphipathic sequences based on...
Enterococcus faecalis Phosphatidylcholines Erythrocytes Amino Acid Sequence Pseudomonas aeruginosa Keratinocytes Peptidomimetics Phosphatidylglycerols Stereoisomerism Female Acinetobacter baumannii Escherichia coli Humans Animals Anti-Bacterial Agents Hemolysis Methicillin-Resistant Staphylococcus aureus Microbial Sensitivity Tests Lipid Bilayers Mice, Inbred BALB C
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ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning.

The New phytologist Dec 15, 2017
The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate betwee...
Machine Learning Proteomics Amino Acid Sequence Conserved Sequence Amino Acid Motifs Protein Sorting Signals Oomycetes Plant Proteins Fungal Proteins Cysteine
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isGPT: An optimized model to identify sub-Golgi protein types using SVM and Random Forest based feature selection.

Artificial intelligence in medicine Nov 26, 2017
The Golgi Apparatus (GA) is a key organelle for protein synthesis within the eukaryotic cell. The main task of GA is to modify and sort proteins for transport throughout the cell. Proteins permeate through the GA on the ER (Endoplasmic Reticulum) fac...
Oligopeptides Golgi Apparatus Animals Computational Biology Support Vector Machine Proteins Databases, Protein Amino Acid Sequence Humans Reproducibility of Results
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Classification of G-protein coupled receptors based on a rich generation of convolutional neural network, N-gram transformation and multiple sequence alignments.

Amino acids Nov 18, 2017
Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithm...
Machine Learning Algorithms Reproducibility of Results Neural Networks, Computer Amino Acid Sequence Sequence Alignment Sequence Analysis, Protein Models, Theoretical Databases, Protein Receptors, G-Protein-Coupled
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Specific and intrinsic sequence patterns extracted by deep learning from intra-protein binding and non-binding peptide fragments.

Scientific reports Nov 2, 2017
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins. Here we sh...
Algorithms Protein Conformation Databases, Protein Deep Learning Binding Sites Peptide Fragments Protein Binding Amino Acid Sequence Proteins
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MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

Journal of theoretical biology Oct 16, 2017
MOTIVATION: Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that p...
Amino Acid Sequence Protein Binding Intrinsically Disordered Proteins Algorithms Binding Sites Computational Biology Models, Theoretical Support Vector Machine Protein Domains
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SkipCPP-Pred: an improved and promising sequence-based predictor for predicting cell-penetrating peptides.

BMC genomics Oct 16, 2017
BACKGROUND: Cell-penetrating peptides (CPPs) are short peptides (5-30 amino acids) that can enter almost any cell without significant damage. On account of their high delivery efficiency, CPPs are promising candidates for gene therapy and cancer trea...
Cell-Penetrating Peptides Computational Biology Internet Amino Acid Sequence
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The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein.

Angewandte Chemie (International ed. in English) Oct 10, 2017
Many intrinsically disordered proteins (IDP) that fold upon binding retain conformational heterogeneity in IDP-target complexes. The thermodynamics of such fuzzy interactions is poorly understood. Herein we introduce a thermodynamic framework, based ...
Circular Dichroism Thermodynamics Protein Binding Protein Folding Calorimetry Fuzzy Logic Amino Acid Sequence Kinetics Models, Molecular Intrinsically Disordered Proteins Molecular Dynamics Simulation
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