How do you define a good binding pose between a protein and a ligand?

Stellamaris Ruth Sotomayor @Stellamaris_Sotomayor

03 March 2017 1 5K Report

What do you think is a good binding pose between a protein and a ligand?

What does it have to have to be defined as a good binding pose?

What is your definition of a good pose?

Stellamaris Ruth Sotomayor

Thank you so much for your help!

I really appreciate it! The articles are very good and useful!

Badges
Science topic

More Stellamaris Ruth Sotomayor's questions See All

¿What is a DUD-E decoy?

The DUD-E paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3405771/ says that their decoys have similar physicochemical properties but different 2-D topologies in relation to the ligands. ¿What...

08 September 2017 8,942 2 View

How do you interpret enrichment factor in virtual screening studies?

Dear colleagues, How would you interpret an enrichment factor of 5 that resulted from the evaluation of a molecular docking strategy? Would it mean that within methodology you find 5 times more...

05 June 2017 5,878 3 View

Is it possible to separate scoring and ranking in Glide?

Dear colleagues, I have read the Glide user guide (https://isp.ncifcrf.gov/files/isp/uploads/2010/07/gli55_user_manual.pdf) but I am a little bit confused. Is it possible to just calculate the...

04 May 2017 8,286 5 View

How do you interpret the solvent-accessible surface area (SASA) score?

I am trying to calculate SASA scoring function using dock 6.7. However, I am confused about the interpretation of the score. I have obtained: SA_Descriptor Score: 14.15 How could I interpret it?...

04 May 2017 7,566 4 View

Is there a way to work with a database instead of working with separate files in Autodock?

Good afternoon, I was wondering if Is there a way to work with a database instead of working with separate files in Autodock? It is computationally expensive to do a process file by file. Since...

03 April 2017 8,669 4 View

Where could I find the pairwise GB grids and the SA grids to do the calculation of the Zou GB/SA scoring function?

I am starting in the molecular docking field. I would like to have some help about this question. I have generated the grid.cnt, grid.ngr, grid.bmp files but I dont know where can I find or how...

01 February 2017 8,601 2 View

How to create a new atom type in Dock6?

Hello :) I have obtained this error during amber file preparation: FATAL: Atom .R.A does not have a type.FATAL: Atom .R.A does not have a...

01 February 2017 1,581 2 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Is it possible to use the Fused Deposition Modeling (FDM) to additively manufacture interconnected porous structure generation of >100-200 micrometer?

Usually, additive manufacturing techniques like SEBM, SLS, and SLM are used for interconnected porous lattice structure generation with sizes of >100–200 micrometers. Can the Fused Deposition...

09 August 2024 7,892 0 View

How to define an anisotropic material with asymmetric elastic compliance/stiffness matrix in ANSYS APDL?

I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...

09 August 2024 5,048 2 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

How to calculate CCS for Sodiated adduct ions and Multiply Charged Ions?

I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...

08 August 2024 8,329 0 View

How can I apply boundary conditions in an orthotropic steel deck numerical model using ABAQUS software?

I am trying to simulate vehicular loading on an orthotopic steel deck bridge section in ABAQUS software. The red arrow mark in the attached figure indicates the direction in which the vehicle will...

08 August 2024 719 0 View