Solvent accessibility of a GPCR transmembrane domain probed by in-membrane chemical modification (IMCM).
Sign Up to like & getrecommendations! Published in 2023 at "FEBS letters"
DOI: 10.1002/1873-3468.14627
Abstract: G protein-coupled receptors (GPCRs) transmit signals from drugs across cell membranes, leading to associated physiological effects. To study the structural basis of the transmembrane signaling, in-membrane chemical modification (IMCM) has previously been introduced for 19… read more here.
Keywords: imcm; transmembrane; membrane chemical; solvent accessibility ... See more keywords
How is structural divergence related to evolutionary information?
Sign Up to like & getrecommendations! Published in 2018 at "Molecular phylogenetics and evolution"
DOI: 10.1016/j.ympev.2018.06.033
Abstract: The analysis of evolutionary information in a protein family, such as conservation and covariation, is often linked to its structural information. Multiple sequence alignments of distant homologous sequences are used to measure evolutionary variables. Although… read more here.
Keywords: structural information; information; structural divergence; evolutionary information ... See more keywords
Gaussian network model can be enhanced by combining solvent accessibility in proteins
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/s41598-017-07677-9
Abstract: Gaussian network model (GNM), regarded as the simplest and most representative coarse-grained model, has been widely adopted to analyze and reveal protein dynamics and functions. Designing a variation of the classical GNM, by defining a… read more here.
Keywords: solvent accessibility; gnm; parameter free; model ... See more keywords
High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5′-OH-end linker and unique 3′-P-end fragments from hydroxyl radical cleavage
Sign Up to like & getrecommendations! Published in 2022 at "RNA Biology"
DOI: 10.1080/15476286.2022.2145098
Abstract: ABSTRACT Given the challenges for the experimental determination of RNA tertiary structures, probing solvent accessibility has become increasingly important to gain functional insights. Among various chemical probes developed, backbone-cleaving hydroxyl radical is the only one… read more here.
Keywords: hydroxyl radical; rtcb ligation; ligation fixed; end ... See more keywords
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac112
Abstract: Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of… read more here.
Keywords: tertiary structures; structures functions; experimental computational; accessibility ... See more keywords
Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa652
Abstract: MOTIVATION RNA solvent accessibility, similar to protein solvent accessibility, reflects the structural regions that are accessible to solvents or other functional biomolecules, and plays an important role for structural and functional characterization. Unlike protein solvent… read more here.
Keywords: rna solvent; dilated convolutional; rnasnap2; accessibility ... See more keywords
SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac019
Abstract: MOTIVATION Accurately predicting protein secondary structure and relative solvent accessibility is important for the study of protein evolution, structure, and an early-stage component of typical protein 3D structure prediction pipelines. RESULTS We present a new… read more here.
Keywords: structure; secondary structure; protein secondary; relative solvent ... See more keywords
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty876
Abstract: MOTIVATION The de novo prediction of RNA tertiary structure remains a grand challenge. Predicted RNA solvent accessibility provides an opportunity to address this challenge. To the best of our knowledge, there is only one method… read more here.
Keywords: solvent accessibility; improved sequence; rna solvent; sequence profiles ... See more keywords
Developing structural profile matrices for protein secondary structure and solvent accessibility prediction
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz238
Abstract: MOTIVATION Predicting secondary structure and solvent accessibility of proteins are among the essential steps that preclude more elaborate 3D structure prediction tasks. Incorporating class label information contained in templates with known structures has the potential… read more here.
Keywords: structural profile; secondary structure; structure; solvent accessibility ... See more keywords
IGPRED-MultiTask: A Deep Learning Model to Predict Protein Secondary Structure, Torsion Angles and Solvent Accessibility
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2022.3191395
Abstract: Protein secondary structure, solvent accessibility and torsion angle predictions are preliminary steps to predict 3D structure of a protein. Deep learning approaches have achieved significant improvements in predicting various features of protein structure. In this… read more here.
Keywords: deep learning; secondary structure; structure; solvent accessibility ... See more keywords
Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.
Sign Up to like & getrecommendations! Published in 2017 at "RNA"
DOI: 10.1261/rna.057364.116
Abstract: As most RNA structures are elusive to structure determination, obtaining solvent accessible surface areas (ASAs) of nucleotides in an RNA structure is an important first step to characterize potential functional sites and core structural regions.… read more here.
Keywords: scale characterization; genome scale; accessibility; accessibility prediction ... See more keywords