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Questions related from Senal Dinuka
I have been performing a steered MD simulation on a ligand unbinding from a DNA. I have read through several publications and have come up only few which follows a similar scope. I have...
22 June 2020 358 0 View
I am working on the well studied glucosidase - cancer relationship. During the work I have come across that beta-glucosidase is less abundant in cancer cells nevertheless human cytoplasm where...
23 October 2019 5,563 2 View
Dear fellow researchers, I have been studying potency of several phytoconstituent of Ayurveda medicinal plants against acetycholinesterase enzyme using a computational approach. I have understood...
23 April 2019 6,492 0 View
Dear fellow researchers, I have performed a transition state search for a suggested reaction coordinate at B3LYP/6-311+G** and was able to identify and confirm both the reactant and products...
02 September 2018 4,197 9 View
I was able to model the first step of proposed hydrolysis mechanism (Koshland et al.) for a cyanogenic beta glucoside and couple of its analogs including a alpha anomer. I identified the...
18 August 2018 8,526 3 View
How would you recommend using semi-emperical method for a TS search and property calculation including verification of the TS using ab intio method?
28 April 2018 4,975 5 View
I am trying to model a transition state (TS) for the RDS of well known beta-glucoside hydrolysis reation pathway. I have tried modelling guess structures and so far wasn't able to achieve desired...
13 April 2018 7,314 4 View
I have been carrying out a transition state optimization with 6-31G* and 6-311G** levels of theory simultaneously. On looking at the Spartan verbose output, it showed to be "ABRIDGED". Does this...
12 January 2018 7,860 1 View
I have been using Amber16 MD suite. As far as I have come a across respgen program in the suite only supports Gaussian output file as the preliminary input. Due to the fact that I follow Spartan...
21 October 2017 6,024 1 View
Dear Research gate Users, I have so far used AutoDock4, AutoDock Vina, GEMDOCK, DOCK and GOLD docking and VS suits. But each an everyone of the software would predict significant change in binding...
26 April 2017 6,696 4 View
Is there a method to find theoretical Ic 50 values for an in silico study. I have obtained binding free energies for several ligand protein complexes. I want to know whether is it possible to...
26 March 2017 6,843 7 View
For MD Simulated protein-ligand complex I have extracted the ligand and the reacting residues(as mentioned in literature) for further kinetic study. I have imported this model to spartan software...
01 January 1970 9,498 6 View
