21 Questions 17 Answers 0 Followers
Questions related from Sheikh Sunzid Ahmed
Dear Scientists I have complete my masters focusing on Drug design and Vaccine Design In Silico. I am highly interested in developing bioinformatic tools (Web Based) for my own use, for example...
09 May 2023 8,195 5 View
I am trying to design a vaccine candidate, for my B-lymphocyte epitopes I want to predict solubility. These peptides are 12 Amino acids long. Is there any server or tool to do that? I have tried...
12 February 2023 8,061 1 View
Dear Experts I need a list of specifications/components list for setting up a Desktop computer to do molecular dynamics simulation. The main purpose is to do Structure Based Drug Design and...
24 January 2023 9,090 3 View
I am performing molecular dynamics simulation in GROMACS for a protein-ligand (Phytochemical) complex using GROMACS via Simlab (Online). Currently they provide only 50 ns simulation. I need 100...
24 December 2022 2,105 4 View
I want to calculate Homo Lumo energy gap using ORCA for my lead candidate (drug design project in silico). But my lead is still on run in ORCA it is over 6 hours (Pentium dual core 2.8 Ghz, 4GB...
04 November 2022 4,101 6 View
I want to perform a phylotranscriptome analysis. For that I have downloaded RNA-seq data from SRA. In galaxy I have trimmed my data, then did assembly through trinity to get contigs from reads....
23 July 2022 9,368 2 View
I want to reconstruct phylogeny using RNA-seq data. I have downloaded the fasta file from SRA of NCBI. It contains paired reads (ILLUMINA HISEQ 2000). I want to construct the full transcriptome to...
22 July 2022 8,861 1 View
I have performed molecular docking and in the interaction diagram of the protein-phytochemical complex, only hydrophobic bonds are there, no hydrogen bonds are involved with any residues of the...
15 July 2022 4,154 5 View
Dear group members, I am doing classical taxonomy (Taxonomic Revision) with DNA fingerprinting. I have learned Computer Aided Drug design to some extent. Now in my thesis, I want to incorporate my...
19 May 2022 9,902 1 View
I am working on Hepatitis B virus, in my current study some marine compounds showed -6.5 kcal/mol affinity in AutoDock Vina, where my positive control Baraclude (antiviral drug) gave -6.2...
16 April 2022 8,597 3 View
If a receptor is new, no data in PDB, literature regarding its active site, Should I perform blind docking?? If a receptor is new , model is in PDB, ligand bounded, then should I perform docking...
15 April 2022 1,872 2 View
Particle gene gun bombardment technique is a direct method of gene transfer. This is used profusely for monocot (angiosperm) transformation, can I use this method for transforming chloroplast of...
26 December 2021 3,324 1 View
How to bring precision and accuracy in writing taxonomic description of plants when the description is nearly absent in relevant literature? Please help Thanks Sunzid
15 November 2021 8,434 4 View
Like minimizing the energy of a 3D predicted hypothetical protein should I need to minimize/ refine the ligand also for optimum molecular docking? Please help. Thanks ---Sunzid
20 October 2021 6,885 3 View
GalaxyRefine is for refinement of single chain 3D structure. I normally use YASARA energy minimization to ensure stability of my predicted protein. Now if I want to use GalaxyRefine for energy...
19 October 2021 8,264 3 View
After performing docking for my hypothetical protein with ligand from PDB experimentally confirmed structure, do I need to validate my docking study. Do I need to redock the PDB ligand with PDB...
19 October 2021 9,987 8 View
I have performed molecular docking and found 9th conformation is the best for me as it has the minimum amount of binding energy. Now I want to save it for using later analysis in BioVia Discovery...
18 October 2021 7,393 5 View
I have developed a 3D model using Modeller. I have minimized its energy using YASARA energy minimizer. Now I weant to know about its docking. For docking, I need to select ligand as I want to make...
10 October 2021 7,760 5 View
As it has been said that impact factor should be considered with the same filed not between different fields, what is considered good impact factor for plant taxonomy? I assume it will not be very...
17 September 2021 6,618 3 View
I want to make a personal research on my local flora and I don't want to use lab facilities this time except examining the herbarium specimen, for that I need to make voucher specimen to identify...
18 August 2021 268 4 View
To take a barcoding approach I need to amplify rbcL/matK/ITS of Sterculia villosa and some other members of Sterculiaceae (Chronquist, 1981). How should I select a suitable primer for a particular...
10 August 2021 8,673 3 View