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Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators.
PeerJ
October 2023
Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, NanJing, China.
Background: Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9.
View Article and Find Full Text PDFAccurate Estimation of Solvent Accessible Surface Area for Coarse-Grained Biomolecular Structures with Deep Learning.
J Phys Chem B
August 2021
National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.
Coarse-grained (CG) models of biomolecules have been widely used in protein/ribonucleic acid (RNA) three-dimensional structure prediction, docking, drug design, and molecular simulations due to their superiority in computational efficiency. Most of these applications strongly depend on the reasonable estimation of solvation free energy, which requires the accurate calculation of solvent accessible surface area (SASA). Although algorithms for SASA calculations with all-atom protein and RNA structures have been well-established, accurately estimating the SASA based on CG structures is extremely challenging.
View Article and Find Full Text PDFProtein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models.
Bioinformatics
December 2019
Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
Motivation: Given the importance of protein-ribonucleic acid (RNA) interactions in many biological processes, a variety of docking algorithms have been developed to predict the complex structure from individual protein and RNA partners in the past decade. However, due to the impact of molecular flexibility, the performance of current methods has hit a bottleneck in realistic unbound docking. Pushing the limit, we have proposed a protein-ensemble-RNA docking strategy to explicitly consider the protein flexibility in protein-RNA docking through an ensemble of multiple protein structures, which is referred to as MPRDock.
View Article and Find Full Text PDFBioMe: biologically relevant metals.
Nucleic Acids Res
July 2012
University of Zagreb, Faculty of Electrical Engineering and Computing, Unska 3, HR 10000 Zagreb, Croatia.
In this article, we introduce BioMe (biologically relevant metals), a web-based platform for calculation of various statistical properties of metal-binding sites. Users can obtain the following statistical properties: presence of selected ligands in metal coordination sphere, distribution of coordination numbers, percentage of metal ions coordinated by the combination of selected ligands, distribution of monodentate and bidentate metal-carboxyl, bindings for ASP and GLU, percentage of particular binuclear metal centers, distribution of coordination geometry, descriptive statistics for a metal ion-donor distance and percentage of the selected metal ions coordinated by each of the selected ligands. Statistics is presented in numerical and graphical forms.
View Article and Find Full Text PDF[The concept and history of biomarker].
Nihon Rinsho
May 2012
Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University.
Biomarker is a characteristic objectively measured and an indicator of biological process. This term indicates not only biological substance, for example protein, ribonucleic acid but also imaging assays. Disease biomarkers have been applied to a wide variety of clinical areas, including oncology, metabolic disorders, neurological disease and immune dysregulation.
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