How to refine a protein-drug complex structure coordinates?

More Francisco J. Enguita's questions See All

Do you have a template for miRNA qPCR arrays from Qiagen (former Exiqon)?

Dear colleagues After a lot of struggle with the new rebranding of Exiqon that sold the LNA technology to Qiagen, we decided to give a try to the new miRNA qPCR arrays. We bought the whole...

11 December 2019 7,166 3 View

RNAse R... which supplier?

Dear All I am looking forward to treat my total RNA samples with RNAse R. Any suggestions about which supplier do you prefer for purchasing it?. Thanks. Best

09 October 2018 9,518 5 View

How to over-express a selected circular RNA?

Dear All Do you have experience in methods for the over-expression of selected circular RNAs in human or mouse cells?... If yes... which strategy did you use?... which vectors and...

06 July 2018 7,681 1 View

What is your favourite Gene-enrichment analysis in a graphical environment?

Hi there I would like to know and to get your feedback about you favourite Gene-enrichment analysis software based in a graphical environment, preferably on-line. Please give me your feedback...

05 June 2018 9,060 9 View

How is the performance of Nanostring system to detect extracellular miRNAs?

Dear All I wanted to give a try to Nanostring system to detect extracellular miRNAs in a screening-based approach. I am wondering if some of you have experience with Nanostring in the detection...

05 June 2018 7,635 3 View

Someone has experience with the new Exiqon-Qiagen miRNAnome qPCR screening panels?

Dear All I had used for a while the Exiqon miRNAnome panels based on low density qPCR arrays. However, since the begginning of this 2018, Exiqon has joined Qiagen. I ordered the same screenings...

01 February 2018 2,140 16 View

How to compare two XPM contact matrices generated by GROMACS?

Hi there I got several contact matrices in XPM format generated by GROMACS trajectories for a series of protein mutants. How to compare them to extract the differences between atom contacts in...

11 December 2017 8,959 12 View

Any web-based tool to get statistics about location and miRNA expression?

Hi there I am dealing with a long list of miRNAs... I would like to get some tool to organize them by functional groups, clusters, chromosome location, tissue expression, etc... Any suggestion?....

09 October 2017 8,554 4 View

Is there any alternative to Green A Dyematrex gel (Amicon) for pseudo-affinity chromatography?

I am trying to reproduce an old purification protocol from 2004 that claims the use of a pseudo-affinity chromatography based on Green A Dyematrex gel (Amicon). The product is discontinued from...

08 September 2016 1,990 3 View

Any tool for the analysis of coarse-grained MD trajectories with NAMD?

Dear All I have several MD trajectories generated by NAMD using coarse-grained dynamics. I would like to perform a deep analysis of the data. Is there any specific tool for this kind of...

01 February 2016 4,894 7 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

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

GC-MS retention index prediticon?

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

08 August 2024 7,403 2 View

I need JCPDS file of LSFCO nanomaterial. Can anyone provide me?

Require for Rietveld refinement in XRD.

08 August 2024 3,081 2 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

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Can you suggest reliable sources defining "3D mesh" and "3D city models"?

Dear fellow researchers, I am currently working on a paper where I need to provide a reliable reference that defines and distinguishes between 3D mesh models and 3D city models. Although I am...

06 August 2024 9,986 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 1,495 2 View

Ramin Ekhteiari Salmas

A short MD simulation can be a good option to relax the binding domain.

You may continue the simulation until to get a stable RMSD values for the ligand (drug).

It depends to what you mean from equilibration - if your system is not in a good mood (has higher total energy or some overlapped atoms or it's embedded inside a membrane atoms) it's better to equilibrate it by a short minimization or a short simulation with some harmonic constraints if it needs.