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I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding interactions and the strengths of bonding regions. I was wondering if there was any type of software that would allow me to analyse this protein and its interactions with swainsonine? I have seen many images like the one below in research papers, but I’m never sure what software the researchers are using to generate these models.

family 5 glycoside hydrolase

Liberato, M. V. et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci. Rep. 6, 23473; doi: 10.1038/srep23473 (2016).

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  • $\begingroup$ This appears to be a bioinformatics question rather than one about biology. $\endgroup$ – tyersome Aug 21 at 0:08
  • $\begingroup$ I know it is rather dense, but the methods section of the paper you cite indicates how the simulations were performed. If you search this site you will find a number of other questions about straight protein molecular modelling software. $\endgroup$ – David Aug 21 at 7:59
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I don't know precisely what you mean by "analyze", which could be anything from simply "view" or "measure distances", to evaluating an energy function on a crystal structure or molecular dynamics simulation, to prediction of binding sites de novo. The tools are different for each case, though some can do several things.

For simply viewing, measuring distances, and creating "pretty pictures" like the ones you included with the question, PyMOL and UCSF Chimera are the most popular tools. Chimera is highly scriptable and can perform molecular dynamics simulations (i.e. simulate movement of atoms based on an energy function), though its capability in this regard is somewhat limited. The NAMD/VMD software suite (which was used in the study cited in the question) is more full-featured, as is CHARMM (the latter of which is also the name of an energy function). For prediction of binding sites de novo (without a bound experimental structure), i.e. "docking", there are DOCK and AutoDock (both with long academic histories) as well as more industry-oriented ones like Glide.

Be careful though what you're getting into — while simply viewing structures and making geometric statements by direct observation is well within reach of the average biochemist with reasonable knowledge of protein structure (provided you trust the lab that solved the structure in the first place!), simulation of proteins using energy functions requires considerable computational expertise, though the "black box" nature of some software glosses over this. It may be relatively easy to run a simulation using questionably appropriate parameters, but the adage "garbage in garbage out" applies very much here. This is somewhat true with docking as well.

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    $\begingroup$ +1 for the last paragraph alone $\endgroup$ – canadianer Aug 21 at 2:12
  • $\begingroup$ A good answer, but be careful about statements of which tools are most popular. You do not mention Jmol, which is one of the viewers available on PDB and is quite powerful. Also, you could enhance your answer with links to the software. $\endgroup$ – David Aug 21 at 7:48
  • $\begingroup$ I have edited your answer to add that the NAMD method was used in the study cited in the question. You can revert my edit if you wish, but improving questions and answers is a valid part of the SE model (although should be used with care). $\endgroup$ – David Aug 21 at 7:55
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I'm not an expert but a start could be PyMOL https://pymol.org/2/ Unfortunately, you need a license to use the latest version

An earlier (free) version can be found here:https://sourceforge.net/projects/pymol/files/latest/download

A tutorial can be found here:https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners

Hope that helps to start!

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