avatarLucianoSphere (Luciano Abriata, PhD)

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Abstract

he release of AlphaFold, by Deepmind itself and also by lots of researchers all around the world:</li></ul><div id="5922" class="link-block"> <a href="https://towardsdatascience.com/alphafold-2-spin-offs-three-months-after-its-official-release-90c2d8714757"> <div> <div> <h2>AlphaFold 2 spin-offs three months after its official release</h2> <div><h3>A summary of the most important works related to AlphaFold 2 to date.</h3></div> <div><p>towardsdatascience.com</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/)"></div> </div> </div> </a> </div><ul><li>Not exactly on modeling protein structures, but on predicting their stability changes upon mutation:</li></ul><div id="0bb1" class="link-block"> <a href="https://lucianosphere.medium.com/why-is-it-so-difficult-to-predict-the-changes-in-stability-that-result-when-a-protein-is-mutated-2df96b2037c5"> <div> <div> <h2>Paper summary: Why is it so difficult to predict the changes in stability that result when a…</h2> <div><h3>Louis and Abriata. Molecular Biotechnology 2021 [open access here]</h3></div> <div><p>lucianosphere.medium.com</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/)"></div> </div> </div> </a> </div><h1 id="af32">Peer-reviewed articles</h1><ul><li>My three CASP 12 papers -times when I was an assessor for CASP:</li></ul><div id="ca5c" class="link-block"> <a href="https://pubmed.ncbi.nlm.nih.gov/29044714/"> <div> <div> <h2>Definition and classification of evaluation units for tertiary structure prediction in CASP12…</h2> <div><h3>For assessment purposes, CASP targets are split into evaluation units. We herein present the official definition of…</h3></div> <div><p>pubmed.ncbi.nlm.nih.gov</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*I08-P0ae_spARohC)"></div> </div> </div> </a> </div><div id="673c" class="link-block"> <a href="https://pubmed.ncbi.nlm.nih.gov/29139163/"> <div> <div> <h2>Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact…</h2> <div><h3>We present our assessment of CASP12 modeling efforts for targets with no obvious templates of high sequence/structure…</h3></div> <div><p>pubmed.ncbi.nlm.nih.gov</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*Rjl3h6FfZwtrpxss)"></div> </div> </div> </a> </div><div id="630a" class="link-block"> <a href="https://pubmed.ncbi.nlm.nih.gov/29235142/"> <div> <div> <h2>Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small…</h2> <div><h3>Integrative modeling approaches attempt to combine experiments and computation to derive structure-function…</h3></div> <div><p>pubmed.ncbi.nlm.nih.gov</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*pDPHe28GA0TE-GSF)"></div> </div> </div> </a> </div><ul><li>My CASP 13 assessment of hard target modeling -when AlphaFold 1 came into the competition (and “won”):</li></ul><div id="d75b" class="link-block"> <a href="https://pubmed.ncbi.nlm.nih.gov/31344267/"> <div> <div> <h2>A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for…</h2> <div><h3>We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure…</h3></div> <div><p>pubmed.ncbi.nlm.nih.gov</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*rFIhiOJDQM6Qb3Fl)"></div> </div> </div> </a> </div><ul><li>A practical summary of the best protein modeling servers from CASP13:</li></ul><div id="da40" class="link-block"> <a href="https://academic.oup.com/bib/article/22/3/bbaa139/5870389">

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            <h2>State-of-the-art web services for de novo protein structure prediction</h2>
            <div><h3>Abstract. Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of…</h3></div>
            <div><p>academic.oup.com</p></div>
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    </div><ul><li>The community of molecular modelers and simulators must share models:</li></ul><div id="7370" class="link-block">
      <a href="https://pubmed.ncbi.nlm.nih.gov/32053168/">
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            <h2>About the need to make computational models of biological macromolecules available and discoverable…</h2>
            <div><h3>About the need to make computational models of biological macromolecules available and discoverable</h3></div>
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About the need to make computational models of biological macromolecules available and discoverablepubmed.ncbi.nlm.nih.gov</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*Ltq89r2R9XxqN12N)"></div> </div> </div> </a> </div><ul><li>Two takes not on modeling protein structures from scratch but about simulating their dynamics:</li></ul><div id="863e" class="link-block"> <a href="https://pubmed.ncbi.nlm.nih.gov/26023027/"> <div> <div> <h2>Assessing the potential of atomistic molecular dynamics simulations to probe reversible…</h2> <div><h3>1 Laboratory for Biomolecular Modeling, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and…</h3></div> <div><p>pubmed.ncbi.nlm.nih.gov</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*YVLzzKKHb4sgs6z5)"></div> </div> </div> </a> </div><div id="2444" class="link-block"> <a href="https://www.sciencedirect.com/science/article/pii/S2001037021001628"> <div> <div> <h2>Assessment of transferable forcefields for protein simulations attests improved description of…</h2> <div><h3>Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses…</h3></div> <div><p>www.sciencedirect.com</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*YCt6m5y4DkVn2eUD)"></div> </div> </div> </a> </div><ul><li>And this one again not about predicting protein structures, but about predicting their stability changes upon mutation:</li></ul><div id="ca9e" class="link-block"> <a href="https://link.springer.com/article/10.1007/s12033-021-00349-0"> <div> <div> <h2>Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the…</h2> <div><h3>Predicting the effects of mutations on protein stability is a key problem in fundamental and applied biology, still…</h3></div> <div><p>link.springer.com</p></div> </div> <div> <div style="background-image: url(https://miro.readmedium.com/v2/resize:fit:320/0*3OFxdWUoOWciNSm7)"></div> </div> </div> </a> </div><p id="9e60">Have a job for me about protein modeling, bioinformatics, protein design, molecular modeling, of protein biotechnology? <a href="https://lucianoabriata.altervista.org/office/contact.html">Contact me here</a>!</p><p id="9b11"><a href="https://www.lucianoabriata.com/"><b><i>www.lucianoabriata.com</i></b></a><i> I write and photoshoot about everything that lies in my broad sphere of interests: nature, science, technology, programming, etc. <a href="https://lucianosphere.medium.com/membership"><b>Become a Medium member</b></a> to access all its stories (affiliate links of the platform for which I get small revenues without cost to you) and <a href="https://lucianosphere.medium.com/subscribe"><b>subscribe to get my new stories</b></a><b> by email</b>. To <b>consult about small jobs</b> check my <a href="https://lucianoabriata.altervista.org/services/index.html"><b>services page here</b></a>. You can <a href="https://lucianoabriata.altervista.org/office/contact.html"><b>contact me here</b></a><b>.</b></i></p></article></body>

AS OF FEBRUARY 2022

Here are all my peer-reviewed and blog articles on protein modeling, CASP, and AlphaFold 2

I compiled here all my peer-reviewed articles (some papers, a couple of reviews, one opinion) and blog entries about modeling proteins without templates, the best tool out there so far (AlphaFold 2), and the contest on structure prediction that positioned its developer Deepmind at the top (CASP).

I preceded each link with a very short summary of the key points inside.

Blog entries

  • About CASP, the Critical Assessment of Structure Prediction:
  • A specific application of AlphaFold 1-like methods to experimental structure determination:
  • The first Colab notebooks enabling everybody to run AlphaFold 2:
  • The AlphaFold — EBI database that aims to cover all proteomes with structural models:
  • MMSEQS-ColabFold, probably the most widely used form of AlphaFold:
  • Developments that followed the release of AlphaFold, by Deepmind itself and also by lots of researchers all around the world:
  • Not exactly on modeling protein structures, but on predicting their stability changes upon mutation:

Peer-reviewed articles

  • My three CASP 12 papers -times when I was an assessor for CASP:
  • My CASP 13 assessment of hard target modeling -when AlphaFold 1 came into the competition (and “won”):
  • A practical summary of the best protein modeling servers from CASP13:
  • The community of molecular modelers and simulators must share models:
  • Two takes not on modeling protein structures from scratch but about simulating their dynamics:
  • And this one again not about predicting protein structures, but about predicting their stability changes upon mutation:

Have a job for me about protein modeling, bioinformatics, protein design, molecular modeling, of protein biotechnology? Contact me here!

www.lucianoabriata.com I write and photoshoot about everything that lies in my broad sphere of interests: nature, science, technology, programming, etc. Become a Medium member to access all its stories (affiliate links of the platform for which I get small revenues without cost to you) and subscribe to get my new stories by email. To consult about small jobs check my services page here. You can contact me here.

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