Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?

Molecular Dynamics Simulations of RNA Molecules

a Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic; Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N...

Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition

BACKGROUND Lysine Specific Demethylase (LSD1 or KDM1A) in complex with its co-repressor protein CoREST catalyzes the demethylation of the H3 histone N-terminal tail and is currently one of the most promising epigenetic targets for drug discovery against cancer and neurodegenerative diseases. Models of non-covalent binding, such as lock and key, induced-fit, and conformational selection could he...

DNA conformational energy from molecular dynamics simulations: Toward the understanding of the indirect readout mechanism in protein-DNA recognition

1 Department of Biosciences of Bionformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan 2 Department of Chemistry & Biochemistry, Kyushu University, Fukuoka, 812-8581, Japan 3 Neutron Research Center and Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institute, Kyoto, 619-0215, Japan 4 Graduate School of Information Science, Na...

Incorporating Molecular Dynamics Simulations into Rational Drug Design: A Case Study on Influenza a Neuraminidases

investigating the feasibility of a proposed model for geometric design of deployable arch structures

deployable scissor type structures are composed of the so-called scissor-like elements (sles), which are connected to each other at an intermediate point through a pivotal connection and allow them to be folded into a compact bundle for storage or transport. several sles are connected to each other in order to form units with regular polygonal plan views. the sides and radii of the polygons are...