Sergey Shityakov

16 Questions 40 Answers 0 Followers

Questions related from Sergey Shityakov

Have you ever tried AutoDock for a project in materials science?

We applied the AutoDock algorithm for the project in materials sciences to evaluate the CO2/ sevoflurane adsorption on the SiO2 nanopore. The results indicate that sevoflurane tends to go to the...

06 June 2019 3,044 1 View

Is there an implementation of drug-polymer in silico models?

We have successfully generated the drug-polymer (PET) system for MD simulations with the MM-PBSA/GBSA approach. Is there an implementation of these drug-polymer in silico models to find any...

04 April 2017 2,672 2 View

We are looking for a collaboration to assist us in determining the experimental binding constant for the protein-drug system. Are you interested?

We are finalizing the manuscript where 50 ns MD simulations are presented on general anesthetic propofol bound to human serum albumin due to the drug pharmacokinetics and pharmacodynamics in the...

01 January 2017 9,150 3 View

Who would like to collaborate in the field of materials science?

I am actively looking for potential collaborators in the field of materials science (gas adsorption on different metal-organic frameworks). If you are interested, then contact me. Thank you.

10 October 2016 3,084 4 View

How can I compute a representation of the free energy landscape (FEL) sampled by the trajectories using different initial peptide conformations?

15-residue triosephosphate isomerase peptide was subjected to 50 ns molecular dynamics in order to investigate its free energy that the peptide visited throughout the simulation (3D plot). The...

10 October 2014 5,676 1 View

Has anyone already applied a physiologically based pharmacokinetic two-compartment model for a single oral dose or i.p. injection of pristine SWCNT?

I successfully implemented a two-compartment (gut-blood) mathematical model for a single oral dose (20 mg/kg) to simulate the SWCNT distribution in the blood using intestinal absorption constant...

06 June 2014 4,389 1 View

What is the procedure to evaluate the free energy of solvation for pH-dependent open/close- ring conformations of midazolam?

A restricted Hartree-Fock SCF calculation was performed using Pulay DIIS with geometric direct optimization to evaluate the free energy of reaction in the solution according to Figure.1, where...

06 June 2014 2,370 5 View

Can retroviral vectors based on the foamy viral (FV) backbone efficiently transduce quiescent cells?

Our results indicated that the HIV-1 cPPT element in a foamy viral vector background will lead to a significant reduction of the FV transduction and viral titre in growth-arrested cells due to the...

05 May 2014 4,890 0 View

What is the best molecular graphics software for rendering of lipid membranes?

For a 3D data rendering, I used the VMD modeling software to visualize the POPC lipid membrane and water molecules, which are covering the surfaces of two lipid leaflets.

05 May 2014 2,792 5 View

How do we measure the aggregation VDW energy for multi-walled carbon nanotube conjugated with FITC?

The 1 ns MD simulation in vacuo produced three types of aggregates after the MWCNT-FITC disintegration into the SWCNT and SWCNT-FITC components. The carbon nanotube aggregation ended up with a...

05 May 2014 6,108 9 View

What is the total net charge for the C60 polarized fullerene in a water solution?

I am simulating the MD of C60 with anti_C60 ab (Fab fragment). In my MD simulations, the fullerene charges and qtot (total charge of the molecule) are 0.0 to calculate the electrostatic...

04 April 2014 215 1 View

Could we trust the topologies produced by the PRODRG server or similar on-line topology generators for molecular dynamics simulations?

The PRODRG software is a good starting point for getting topologies for molecular dynamics simulations. However, there are major and minor issues with force-field compatibilities, besides the fact...

04 April 2014 1,185 3 View

Who would like to collaborate in the field of rational drug design and discovery?

VirtualScreenLab (http://shityakovlab.uphero.com) is the computational chemistry & bioinformatics laboratory as part of the blood-brain barrier department (Head: Prof. C. Förster) at the...

03 March 2014 5,373 5 View

Is anyone doing transnational research on human pheromones?

We (http://shityakovlab.uphero.com) have analyzed the androstenone-to-androstadienone conversion as a chemical reaction using the EasyHybrid - GTKDynamo open source software integrated into...

01 January 1970 4,884 1 View

We are actively looking for a collaboration to take part in various scientific projects.

We are actively looking for a collaboration to take part in various projects for AI-based rational drug design and discovery, single-cell sequencing, image processing (not limited to these...

01 January 1970 6,417 2 View

What will happen with the variant surface glycoprotein (VSG) of Trypanosoma brucei at low pH?

We investigate the conformational shift of VSG protein from Trypanosoma brucei, using the experimental (size-exclusion chromatography) and theoretical methodology (Adaptive Poisson-Boltzmann...

01 January 1970 1,745 1 View