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Questions related from Sheikh Sunzid Ahmed
Please help to understand the aims and scopes of these two different techniques along with the possible computational cost that they render. Thanks.
26 April 2024 9,669 2 View
We have assembled a chloroplast genome of angiosperm and submitted the annotated assembly to NCBI GenBank. Within two-working days we got accession number for that submission. GenBank in their...
22 April 2024 9,949 0 View
So far I have found Prof. D. Soltis, Prof. John Cress and Prof. Jim Leebens-Mack. Please share your thinking. Thank you very much.
13 April 2024 5,014 1 View
I did not find IF in the website BioxBio for this journals but in their website they have claimed to have an IF of 5.8. Also did not find IF in the 2022 SCIE list (PDF) released by Web of...
13 April 2024 7,130 2 View
Apart from IMPPAT, TIPDB, MeFSAT and Seaweed metabolite databases, could you please suggest me some more databases for virtual screening study. The target receptor is from...
10 April 2024 2,865 3 View
In their website they mentioned it's IF is 5.8. But in the JIF2022 report, I did not find. Is it because of its inclusion in the Emerging Source Citation Index? and because of not included in the...
08 October 2023 1,028 1 View
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 8,208 5 View
In our recent work we have used FIC values to find the best species against a particular disease. We have docked the bioactive phytochemicals of that particular plant against specific receptor of...
02 April 2023 2,311 2 View
Some potential journals of Hindwai that we want to try - BioMed Research International, Evidence-Based Complementary and Alternative Medicine, Journal of Immunology Research. All these are...
16 March 2023 1,316 2 View
Is it ethically right to assemble a chloroplast or mitochondrial genome from NCBI public data?? Would be very grateful to know, if possible please suggest me some methodology papers for that, I am...
20 February 2023 9,206 1 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 8,070 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 9,102 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 2,115 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 4,109 6 View
I am using Autodock vina, ClusPro, HPEPDOCK for peptide docking . Is there any offline tool that can be used for protein-peptide docking? Thanks in Advance. Sincerely- Sunzid.
23 August 2022 6,584 0 View
After numerical taxonomy analysis, using binary character (morphological trais) states, I have built my UPGMA and NJ tree. Now I want to export the tree in NEWICK /NEXUS format. Earlier I used...
31 July 2022 5,119 0 View
Similarly can all actinomorphic flowers be Regular?? Thanks.
29 July 2022 9,696 2 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 9,380 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 8,876 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 4,165 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 9,916 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 8,605 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 1,880 2 View
Like IMPAAT database of phytochemicals, is there any database specific for fungal compounds that could be used for Structure based drug design study??? Thanks.
30 March 2022 8,770 4 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 3,337 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 8,446 4 View
I have extracted a ligand from PDB native protein and then used that to dock with my hypothetical protein. The hypothetical protein is phosphopantatheinyl transferase and in PDB the crystalized...
21 October 2021 3,211 3 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 6,897 3 View
I have used Swiss Dock but I can't view my 9th conformation/seed9.crd file generated by Swiss Dock in Chimera. So I want to use CB Dock as an alternative of Swiss Dock. Is CB dock reliable for...
20 October 2021 5,145 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 8,279 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 9,996 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 7,407 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 7,771 5 View
I want to make an experiment of Yersinia pestis focusing on homology modeling of one of its hypothetical protein. What would be the minimum percentage of sequence identity for homology modeling?...
19 September 2021 1,009 1 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 6,633 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 278 4 View
If I stay very far away from my lab, how can I study floral morphology of my collected specimen. Should I carry a simple microscope with me during field trip, it seems funny, then what should i do...
18 August 2021 4,180 2 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 8,683 3 View
Xanthosoma violaceum is a member of Araceae (Dastar Kachu in Bengali). It has fleshy leaves. How should I prepare a herbarium sheet for it, like how should I dry the sample, what is the standard...
10 August 2021 3,292 7 View
