AIMC Topic: Nucleic Acid Conformation

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Insights into the Kinetic Partitioning Folding Dynamics of the Human Telomeric G-Quadruplex from Molecular Simulations and Machine Learning.

Journal of chemical theory and computation Aug 25, 2020
The human telomeric DNA G-quadruplex follows a kinetic partitioning folding mechanism. The underlying folding landscape potentially has many minima separated by high free-energy barriers. However, using current theoretical models to characterize this...
Humans Nucleic Acid Conformation G-Quadruplexes Telomere Machine Learning Kinetics Molecular Dynamics Simulation
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CD-NuSS: A Web Server for the Automated Secondary Structural Characterization of the Nucleic Acids from Circular Dichroism Spectra Using Extreme Gradient Boosting Decision-Tree, Neural Network and Kohonen Algorithms.

Journal of molecular biology Aug 22, 2020
Nucleic acids exhibit a repertoire of conformational preference depending on the sequence and environment. Circular dichroism (CD) is an essential and valuable tool for monitoring such secondary structural conformations of nucleic acids. Nonetheless,...
Nucleic Acid Conformation Circular Dichroism Internet Automation Nucleic Acids Neural Networks, Computer Software Algorithms User-Computer Interface Decision Trees
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Synthesis Success Calculator: Predicting the Rapid Synthesis of DNA Fragments with Machine Learning.

ACS synthetic biology Jun 30, 2020
The synthesis and assembly of long DNA fragments has greatly accelerated synthetic biology and biotechnology research. However, long turnaround times or synthesis failures create unpredictable bottlenecks in the design-build-test-learn cycle. We deve...
Machine Learning Software DNA Fragmentation Genome, Bacterial Escherichia coli Plasmids Nucleic Acid Conformation Databases, Genetic DNA
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Predicting RNA SHAPE scores with deep learning.

RNA biology May 31, 2020
Secondary structure prediction approaches rely typically on models of equilibrium free energies that are themselves based on in vitro physical chemistry. Recent transcriptome-wide experiments of in vivo RNA structure based on SHAPE-MaP experiments pr...
Deep Learning Computational Biology Models, Molecular Neural Networks, Computer Codon, Initiator RNA Nucleic Acid Conformation RNA Folding
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ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence.

Journal of molecular biology Mar 4, 2020
The intricate details of how proteins bind to proteins, DNA, and RNA are crucial for the understanding of almost all biological processes. Disease-causing sequence variants often affect binding residues. Here, we described a new, comprehensive system...
Sequence Analysis, Protein Prokaryotic Cells DNA RNA Protein Conformation Nucleic Acid Conformation Binding Sites Eukaryota Protein Binding Computational Biology Proteins Machine Learning Software Animals Humans Neural Networks, Computer
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A generative model for constructing nucleic acid sequences binding to a protein.

BMC genomics Dec 27, 2019
BACKGROUND: Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational...
Base Sequence Algorithms Transcription Factors Humans Nucleic Acid Conformation Proteins Aptamers, Nucleotide DNA Protein Binding Neural Networks, Computer
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Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter.

BMC bioinformatics Dec 24, 2019
BACKGROUND: RNA secondary structure prediction is an important issue in structural bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP-hard problem. Recently, many different machine-learning methods, Markov models, a...
RNA Nucleic Acid Conformation Neural Networks, Computer Base Pairing Thermodynamics
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Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nature communications Nov 20, 2019
A gene is considered essential if loss of function results in loss of viability, fitness or in disease. This concept is well established for coding genes; however, non-coding regions are thought less likely to be determinants of critical functions. H...
Chromatin INDEL Mutation Humans Enhancer Elements, Genetic Genes, Reporter Mutation Computer Simulation Genome, Human Supervised Machine Learning DNA Nucleic Acid Conformation Genetic Variation Gene Expression Introns
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EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame.

PLoS computational biology Jun 27, 2019
Emerging RNA-based approaches to disease detection and gene therapy require RNA sequences that fold into specific base-pairing patterns, but computational algorithms generally remain inadequate for these secondary structure design tasks. The Eterna p...
Video Games Humans Genetic Engineering Neural Networks, Computer RNA Algorithms Nucleic Acid Conformation Sequence Analysis, RNA Crowdsourcing Internet
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DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines.

Journal of chemical information and modeling Apr 16, 2019
Accurate identification of protein-DNA binding sites is significant for both understanding protein function and drug design. Machine-learning-based methods have been extensively used for the prediction of protein-DNA binding sites. However, the data ...
Nucleic Acid Conformation Support Vector Machine Models, Molecular DNA DNA-Binding Proteins Protein Conformation
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