Michał Adam Michałowski

5 Questions 4 Answers 0 Followers

Questions related from Michał Adam Michałowski

What are suggested computational tools/protocols for disulfide bond prediction in protein structure?

I am looking for some tools for disulfide bonds prediction and energy/structure estimation. What I have: patch-clamp results of WT, single and double cysteine mutant of the ionotropic receptor...

01 April 2020 8,844 6 View

Is autodock vina binding affinity related to activation energy?

Autodock Vina calculates "binding affinity" in kcal/mole. Is it somehow connected to activation energy in Arrhenius equation? I am thinking about this equation (for non diffusion limited...

10 January 2018 5,133 3 View

Is Shrodinger suite and NAMD compatible?

Hi! So far I have been preparing my MD systems for NAMD using Modeller and CHARMM-GUI. I am thinking about switching to Schrodinger suite of programs. To perform MD I am using a supercomputing...

09 May 2017 8,758 4 View

What is the theory behind linking low frequency normal modes to protein conformation changes?

Most papers about normal mode analysis are claiming that low frequency normal modes correspond to protein conformation changes. In most cases software visualizes those modes as arrows. However,...

05 October 2016 9,817 3 View

How to dock an ion using autodock vina?

Hi! I want to dock an ion (Cl-) to my protein model using autodock vina. The error is as follows: WARNING atoms have no bonds....BUILDING THEM!!!WARNING atoms have no bonds....BUILDING...

20 June 2016 1,644 4 View