Reza Esmaeeli
A5025577359- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Advanced Electron Microscopy Techniques and Applications
- Enzyme Structure and Function
- Tuberculosis Research and Epidemiology
- Advanced Chemical Physics Studies
- Hydraulic flow and structures
- Machine Learning in Materials Science
- Protein Structure and Dynamics
- Carbohydrate Chemistry and Synthesis
- Water Systems and Optimization
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- Hydrology and Sediment Transport Processes
- Chemical Synthesis and Analysis
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
University of Florida
2021-2024
Interface (United States)
2022-2024
University of Florida Health
2022
University of Maragheh
2020
University of Tehran
2018
Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy functional genome. Yet, our structural understanding of how is limited. We present MELD-DNA, novel computational approach predict the structures protein-DNA complexes. The method combines molecular dynamics simulations general knowledge or experimental information through Bayesian inference. physical model sensitive sequence-dependent properties conformational changes required for binding, while accelerates...
Abstract In the present study, performance of support vector machine for estimating vertical drop hydraulic parameters in presence dual horizontal screens has been investigated. For this purpose, 120 different laboratory data were used to estimate three drop: relative length, downstream depth, and residual energy machine. each parameter, 12 models analyzed by using a The was evaluated with statistical criteria (R2, DC, RMSE) best model introduced parameters. evaluation length equipped...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound protein protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase covalently nucleotide analog, ion channel ORF3a lipid. Sixty-one models submitted from 17 independent research...
In this study, we demonstrate that anion−π interactions (an attractive noncovalent force between electron deficient π-systems and anions) are involved in the stabilization of GAAA GGAG RNA tetraloops. Using single recognition particle (SRP)–RNA complexes as a case combined molecular dynamics (MD) quantum mechanics (QM) calculations to shed light on structural influence phosphate–G hydrogen bonds (HBs) involving K+/Mg2+ water clusters. addition, assemblies herein were further characterized by...
<title>Abstract</title> Adding nucleotide pairs to a DNA alphabet not only increases the linear information density of molecules, but also may increase diversity folds available molecular system. Reported here is an example this. A single additional nucleotide, with 5-nitro-6-aminopyridone ("Z") heterocycle, selected from artificially expanded genetic system (AEGIS), was incorporated at twelve sites into strand 23 nucleotides in length. With fluor its 5'-end and quencher 3'-end, this...
The mycobacterial enzyme pyrazinamidase (PZase) is the target of key tuberculosis drug, pyrazinamide. Mutations in PZase cause drug resistance. Herein, three point mutations, W68G, L85P, and V155G, were investigated through over 8 µs molecular dynamics simulations coupled with essential binding pocket analysis at neutral (pH = 7) acidic 4) ambient conditions. 51-71 flap region exhibited drastic displacement leading to enlargement cavity, especially lower pH. Accessibility solvent active site...
The β subunit of E. coli DNA polymererase III is a sliding clamp associated with increasing the processivity synthesis. In its free form, it circular homodimer structure that can accomodate double-stranded in nonspecific manner. An open state must be accessible before loading DNA. opening mechanism still matter debate, as effect bound on opening/closing kinetics. We use combination atomistic, coarse-grained, and enhanced sampling strategies both explicit implicit solvents to identify events...