AIMC Topic: Protein Domains

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Computational and artificial neural network based study of functional SNPs of human LEPR protein associated with reproductive function.

Journal of cellular biochemistry Jun 25, 2019
Genetic polymorphisms are mostly associated with inherited diseases, detecting and analyzing the biological significance of functional single-nucleotide polymorphisms (SNPs) using wet laboratory experiments is an arduous task hence the computational ...
Receptors, Leptin Infertility Protein Domains Amino Acid Substitution Mutation, Missense Humans Neural Networks, Computer Molecular Docking Simulation Polymorphism, Single Nucleotide
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DeepACLSTM: deep asymmetric convolutional long short-term memory neural models for protein secondary structure prediction.

BMC bioinformatics Jun 17, 2019
BACKGROUND: Protein secondary structure (PSS) is critical to further predict the tertiary structure, understand protein function and design drugs. However, experimental techniques of PSS are time consuming and expensive, and thus it's very urgent to ...
Neural Networks, Computer Proteins Protein Domains Protein Structure, Secondary Algorithms Deep Learning Models, Theoretical
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Predicting drug-target interaction network using deep learning model.

Computational biology and chemistry Mar 25, 2019
BACKGROUND: Traditional methods for drug discovery are time-consuming and expensive, so efforts are being made to repurpose existing drugs. To find new ways for drug repurposing, many computational approaches have been proposed to predict drug-target...
Breast Neoplasms Antineoplastic Agents Support Vector Machine Proteins Databases, Protein Deep Learning Protein Binding Computational Biology Databases, Chemical Genes, Neoplasm Models, Chemical Protein Domains Amino Acid Sequence Drug Repositioning Molecular Structure
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iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.

Proteins Dec 3, 2018
Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning-based methods are gaining increasing momentum in this field. Due to the limited number of experimental data, using...
Proto-Oncogene Proteins c-mdm2 Tumor Suppressor Protein p53 Thermodynamics Binding, Competitive Computational Biology Evolution, Molecular Proteins Models, Molecular Mutation Protein Domains Machine Learning Protein Binding
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Computational discovery of direct associations between GO terms and protein domains.

BMC bioinformatics Nov 20, 2018
BACKGROUND: Families of related proteins and their different functions may be described systematically using common classifications and ontologies such as Pfam and GO (Gene Ontology), for example. However, many proteins consist of multiple domains, a...
Gene Ontology Amino Acid Sequence Molecular Sequence Annotation Algorithms Computational Biology Proteins Databases, Protein Area Under Curve Protein Domains
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SeqSVM: A Sequence-Based Support Vector Machine Method for Identifying Antioxidant Proteins.

International journal of molecular sciences Jun 15, 2018
Antioxidant proteins can be beneficial in disease prevention. More attention has been paid to the functionality of antioxidant proteins. Therefore, identifying antioxidant proteins is important for the study. In our work, we propose a computational m...
Humans Support Vector Machine Software Protein Domains Sequence Analysis, Protein Animals Oxidative Stress
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DPP-PseAAC: A DNA-binding protein prediction model using Chou's general PseAAC.

Journal of theoretical biology May 16, 2018
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting...
Protein Domains Amino Acids DNA-Binding Proteins Amino Acid Sequence Nucleic Acid Conformation Algorithms Databases, Protein Reproducibility of Results DNA Models, Molecular Computational Biology Support Vector Machine
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Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures.

Biology direct Feb 21, 2018
BACKGROUND: The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis and selection of genes used ...
Protein Domains Humans Machine Learning Sequence Analysis, RNA
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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 Intrinsically Disordered Proteins Binding Sites Models, Theoretical Support Vector Machine Algorithms Protein Domains Protein Binding Computational Biology
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A new model of flavonoids affinity towards P-glycoprotein: genetic algorithm-support vector machine with features selected by a modified particle swarm optimization algorithm.

Archives of pharmacal research Dec 27, 2016
Flavonoids exhibit a high affinity for the purified cytosolic NBD (C-terminal nucleotide-binding domain) of P-glycoprotein (P-gp). To explore the affinity of flavonoids for P-gp, quantitative structure-activity relationship (QSAR) models were develop...
ATP Binding Cassette Transporter, Subfamily B, Member 1 Datasets as Topic Flavonoids Protein Binding Models, Chemical Quantitative Structure-Activity Relationship Support Vector Machine Protein Domains
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