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My undergraduate thesis is on the topic "Ligand design from protein-protein interfaces" and my PI has asked me to learn the basics of Structural bioinformatics over the summer so that I'll be able to start with my project as I begin my next semester(last week of July). Can someone please suggest me top resources to learn the basics of structural bioinformatics. Though I have done projects in Genomics, and Systems biology, this will be my first time with structural bioinformatics, so, I'll really appreciate some good leads. Thanks!

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  • $\begingroup$ Hello Akhil, this is not the greatest place for open questions. You could try one of the forums or just google it. $\endgroup$
    – Kamil S Jaron
    Jun 18 '19 at 14:01
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As others have said, there is no short cut and you will need to spend some time with a good book.

I would say there are 3 broad areas of understanding you have to have as a structural bioinformatician:

  • Solid understanding of the basic science. This includes molecular biology but also chemistry, which is often overlooked.
  • Knowledge of the databases and data formats available in the field. You need to know where to go to get protein structures, protein sequences etc.
  • Programming and algorithmic skills. You don't have to be a computer whiz but being effective in a high-level language (e.g. Python, R, Julia) and being able to parse data and carry out basic data analyses are essential.

If you want to take it further and have a bit more time then I would consider implementing something yourself such as a protein secondary structure predictor. Getting this working is challenging and would show you have competency in the above three areas.

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  • $\begingroup$ Thank you. If you could also suggest me some resources(your top picks) for the first two areas, it'll be really helpful. $\endgroup$
    – mrVerma
    Jun 19 '19 at 12:14
  • $\begingroup$ Of the top of my head "Introduction to Protein Structure" by Branden and Tooze is good. In terms of databases have a look at PDB, UniProt, Pfam, CATH and InterPro. $\endgroup$
    – jgreener
    Jun 19 '19 at 16:37
  • $\begingroup$ Thanks @jgreener $\endgroup$
    – mrVerma
    Jun 26 '19 at 13:10
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A good starting point could be this book by Gu and Bourne:

Structural Bioinformatics, 2nd Edition

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  • $\begingroup$ Thanks, I'll check it out. But I was hoping for a good blog or some tutorial(web/video) kind of resource rather than a book $\endgroup$
    – mrVerma
    Jun 18 '19 at 13:52
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    $\begingroup$ @AkhilVerma — Books are far more informative. They contain more information, undergo quality control if published by reputable publishers and are generally better written, more comprehensive and more reliable. You cannot learn anything worthwhile without putting in some effort. Certainly not structural biology. How’s your chemistry, incidentally? You’re going to need that too $\endgroup$
    – David
    Jun 18 '19 at 18:53

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