Sheikh Sunzid Ahmed

43 Questions 21 Answers 0 Followers

Questions related from Sheikh Sunzid Ahmed

DCCM calculation || Molecular dynamics simulation, help please?

I have used desmond of schrodinger to conduct 100 ns simulation for my protein-ligand complex, now want to perform DCCM analysis, to perform it using Bio3D package of R, DCD file is needed....

22 October 2024 5,436 0 View

Is it possible to publish patent for a chloroplast genome of a medicinal plant?

If I follow conventional techniques and assemble a CP genome with annotation, then is it patentable? The Cp genome is the first of its kind and before our assembly, no one did that, and there is...

02 September 2024 753 1 View

What are the key differences between MMGBSA and MMPBSA in estimating free binding energy of a protein-ligand complex following Drug design study?

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 9,985 2 View

How much time does NCBI GenBank takes for public release of complete chloroplast genome sequence?

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 10,026 0 View

Top scientists in the field of Plant Molecular Systematics and Evolution? Could you please provide me a list?

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 5,066 1 View

Bioinformatics and Biology Insights of SAGE, does it have an impact factor?

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 7,232 2 View

Please suggest me some large databases of phytochemicals (plants/algae/fungi) for computer-aided drug design study?

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 2,910 3 View

Bioinformatics and Biology Insights - From SAGE. Does this journal have Impact Factor?

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 1,093 1 View

Should I learn web development as a beginner bioinformatician?? Will it help in long term development??

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 8,262 5 View

Is it okay to add molecular reactivity calculation based on quantum mechanics (DFT HOMO LUMO) in an ethnobotany paper??

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 2,371 2 View

Hindwai should I publish here?? Is it controversial??

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 1,386 2 View

Can I assemble a chloroplast genome if the primary data is not mine?? If I don't do sequencing??

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 9,270 1 View

Is there any server/tool to predict on the solubility of peptides??

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 8,103 1 View

Molecular Dynamics Simulation || Desktop Computer Purchase || Specification Help??

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 9,144 3 View

Can I perform MD simulation for 100 ns in two steps, 50 + 50??

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 2,145 4 View

For DFT Homo Lumo calculation do you need a very powerful computer in the same way as that is needed for Molecular Dynamics Simulation 100 ns??

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 4,139 6 View

Is there any Standalone tool with GUI for windows to perform Protein - Peptide docking ?? Peptide length <50 AA?

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 6,612 0 View

Is there any option to extract dendrogram built in NTSYSpc 2.02e in NEWICK/NEXUS format for further modification?

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 5,171 0 View

Can all Zygomorphic flowers be irregular?

Similarly can all actinomorphic flowers be Regular?? Thanks.

29 July 2022 9,736 2 View

How to assemble contigs? after getting it from reads through Trinity (using RNA-Seq)?

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 9,431 2 View

How can I prepare a single transcriptome from NCBI SRA fasta (reads containing) file (of a single plant species)?

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 8,914 1 View

Can I propose a small molecule as potential lead if it shows only Hydorphobic bonds after docking??

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 4,201 5 View

How plant taxonomy is related with Computer aided drug design??

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 9,951 1 View

If I get binding affinity -6.5 kcal/mol which is greater than my positive control, can I publish this? or do I need more significant finding?

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 8,638 3 View

About the publisher Universe PG?

Dear group members The journal started its journey from 2019. Want to know more about this journal. Please help. Thanks. Sincerely- Sunzid.

16 April 2022 9,839 8 View

When should you perform blind docking and when site specific docking??

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 1,915 2 View

Is there any database for only Fungal compounds that can be used for virtual screening??

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 8,799 4 View

Can I use particle gene gun bombardment technique to transform the chloroplast of Selenastrum capricornutum (Unicellular green algae)?

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 3,379 1 View

How to write a good taxonomic description of plants when it is nearly undescribed or a new record?

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 8,492 4 View

Regarding validation of molecular docking through RAMACHANDRAN plot?

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 3,242 3 View

Should I minimize the energy of ligand also before performing molecular docking?

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 6,955 3 View

Can I use CB Dock as a tool of molecular blind docking for my publication? Is it reliable, if not what are some web based docking tools ?

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 5,204 3 View

Can I use GalaxyRefine as a reliable tool for refinement of my predicted 3d structure of protien and also for my publication??

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 8,348 3 View

Do I really need to validate my model after docking study for publication, especially for Hypothetical protein characterization??

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 10,042 8 View

How to save my pdbqt file with desired pose for the ligand-protein complex, AutoDock is not saving a particular one, instead saving all?

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 7,441 5 View

How to select ligand for molecular docking study of a hypothetical protein?

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 7,813 5 View

What should be the minimum percentage of sequence identity and query coverage for homology modeling of a hypothetical protein?

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 1,042 1 View

What is the average impact factor of Tier 1 Plant Taxonomy Journal? What is considered a good impact factor for taxonomy , what is below average?

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 6,696 3 View

Can I make a Voucher Specimen without an electric dryer?

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 322 4 View

Flower Dissection without the help of Lab?

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 4,209 2 View

Regarding Voucher Specimen and the necessity of stem + leaves -/+ Flower or Fruit?

I want to make voucher specimen with Pterygota alata / Pterospermum acerifolium/ Sterculia villosa/foetida/versicolor/hamiltonii etc. >>>>Sterculiaceae (Chronquist) or Malvaceae (APG...

18 August 2021 2,898 1 View

How to design or select a primer before amplification of rbcL/matK/ITS barcoding region for a particular plant (Sterculia villosa)?

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 8,740 3 View

How to prepare herbarium sheet if the plant sample is very much large, fleshy and succulent?

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 3,323 7 View