How do we use pepfold properly and do we have to use pepfold 3 or 4 for docking and simulaton?

Ahmed Abdelghyoum Mahgoub @Ahmed-Abdelghyoum-Mahgoub

17 April 2024 0 658 Report

i want to use pepfold for epitopes simulation and docking but im not quite familiar with pepfold or docking in the first place, im asking about a clear guide if possible for the section of docking as im not familiar with it?

Badges
Science topic

Similar topics
Psychology

More Ahmed Abdelghyoum Mahgoub's questions See All

I have get this error when i calculated the geometrical optimization for prco3, it takes 12 hours until gives this message in the outputfile?

Fatal error in MPI_Allreduce: Other MPI error, error stack: MPI_Allreduce(1628)......: MPI_Allreduce(sbuf=000002459254A180, rbuf=000002459F86A140, count=4851, MPI_DOUBLE_COMPLEX, MPI_SUM,...

09 August 2024 7,615 1 View

Why Do TDS and EC Increase with Larger Wastewater Volumes, While BOD and COD Decrease?

I have carried out MFC experiments on three different volumes, 50, 500 and 1000 mL of wastewater. Results after MFC treatment shows that TDS and EC are more in larger volumes of water i.e. TDS and...

09 August 2024 9,621 0 View

How to set the environment variable for incorporating the GD3 dispersion in G16 for performing calculations using the OPBE functional?

I have incorporated the dispersion effect for the OPBE functional by specifying the S6, SR6 and S8 parameters for GD3 in Gaussian G09 package. For this purpose, I have defined the environment...

05 August 2024 1,494 2 View

How prion can cause disease?

how is prion can cause disease

01 August 2024 250 1 View

Has anyone used Jump 2 before?

Jump 2 is the 1st app scientifically developed to measure your jump height.

31 July 2024 8,194 0 View

Help on understanding the implementation of Mori Tanaka method on MATLAB?

I am new to Micromechanics and having similar problem with understanding the implementation of the formula's. I would appreciate if anyone can guide me on how to go about getting a scalar value...

30 July 2024 969 0 View

I need a reliable source or an example supported by excel sheet to understand Fuzzy Vikor?

27 July 2024 5,916 1 View

What are the most PROBLEMS of HYBRID nanofluid in oil industry ?

explain your idea

23 July 2024 1,197 0 View

Can anybody provide me the Matlab code to plot the attached picture (Time-Frequency Domain), please?

Time-Frequency Domain

19 July 2024 8,031 2 View

"Hello, I am trying to find public datasets containing FTIR spectra of blood samples (both healthy and disease-related)?

These datasets will be used in the training of machine learning algorithms. Does anyone know any available data?"

17 July 2024 6,519 3 View

Why activated CAR-Jurkat cell could not kill targets?

Previously when I co-coluture anti-CD19(FMC63) CAR-Jurkat with Raji with E:T=5:1, Jurkat can eliminate Raji in 24h. However, when I test another CAR construct, although I can dectect totally CD69...

06 August 2024 640 2 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

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 1,494 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,726 4 View

How to start a Molecular Dynamics Simulation?

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

Which will be the best software for the Hydration shell analysis with molecular dynamics?

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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How to do Mann-Whitney U test with Bonferroni corrected p-values?

Dear All, My lab primarily works on insect wing patterns. In one of the projects, my student and I have defined 19 abnormality characters on the forewing and 6 abnormality characters on the...

31 July 2024 6,464 5 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 780 1 View

How to restart MD without using checkpint file in GROMACS?

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

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

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