I have downloaded an sdf file from zinc but how do i get to know how many molecules are there in a single file, is there any particular software to see it?
We are trying to find the biological correlation between miRNA and certain genes. We found the general correlation through IPA (Ingenuity Pathway Analysis). Thank you for your inputs!
05 June 2019 7,055 6 View
I have mi-RNA sequencing data, where my 3 prime adapter is attached with 12 Nucleotide UMI Sequence (in random manner) along with Reverse Transcriptase primer and Universal Adapter Overall...
31 December 2018 691 5 View
I found an explanation in Schrodinger's knowledge base but i am not sure how to run the python scripts in Ubuntu. If possible kindly suggest an easy way. Huge Thanks
08 September 2018 7,952 3 View
I have a transcription factor protein X and X has a co-activator protein Y. XY bind to the DNA and downstream expression of proteins occur. Now I block the activity of X through inhibitor but dont...
07 August 2018 6,507 7 View
Kindly help me interpreting the graph. I am not sure if the ligand is still intact with protein or it has diffused away.
06 July 2018 2,093 6 View
I want to study the dynamics of ABC transporters along with a peptide molecule which in physiological conditions passes through the transporter. I am clueless how to set the peptide molecule in to...
05 June 2018 6,178 5 View
Hello awesome people, I am new to GROMACS and i have been practicing with different tutorials available online. I successfully ran 1ns simulations. I ran couple of simulations with mdp files as...
01 February 2018 3,665 4 View
I have following doubts in Gromacs ,and want to know if these things are normal? or i am doing something wrong? 1) The protein is outside the solv box ( picture 1). 2) while i am running...
01 February 2018 7,861 5 View
I want to perform protein-protein docking .Please suggest me some software's which can find active site by itself and dock the protein. I have tried HADDOCK but u need to provide active sites in...
08 September 2017 4,725 3 View
I have docked two proteins using patchdock but i am not able to view the P-P interaction in PIC calculator. I doubt there must be something wrong with the PDB files that i have given as input....
08 September 2017 10,032 8 View
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 View
Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...
06 August 2024 1,495 2 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...
03 August 2024 3,371 3 View
I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?
02 August 2024 3,143 4 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar
29 July 2024 3,084 8 View
I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...
28 July 2024 2,979 1 View
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 View
I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...
28 July 2024 7,413 6 View