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_sources/orodjarna/analiza.md

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 Spodaj je zbranih nekaj uporabnih povezav do zbirk in orodij, ki omogočajo analizo makromolekulskih struktur.
 
+## Sekundarna struktura
+
+Orodja za **pripis (*asignacijo*) sekundarne strukture** posameznim aminokislinskim ostankom na osnovi 3D strukture (pogosto jih najdemo integrirana v programe za vizualizacijo struktur ipd.):
+- [STRIDE](https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py) (STRuctural IDEntification), ki kombinira vodikove vezi in njihovo energetiko (glede na geometrijo, s prilagoditvami na osnovi empiričnih podatkov iz znanih struktur) s torzijskimi koti ogrodja {cite:p}`Frishman1995aaa`;
+- [DSSP](https://pdb-redo.eu/dssp) (Dictionary of Secondary Structure of Proteins), ki, podobno kot STRIDE, kombinira vodikove vezi in njihovo energetiko (glede na geometrijo, na osnovi enačbe za izračun elektrostatskega potenciala) {cite:p}`Kabsch1983aaa`.
+
+
+
 ## Lastnosti
 
 - [APBS](https://server.poissonboltzmann.org/): Strežnik na osnovi programa Adaptive Poisson-Boltzmann Solver, ki omogoča izračun **elektrostatskih lastnosti** molekul in ob tem upošteva solvatacijo {cite:p}`Jurrus2018aaa`.

_static/vendor/fontawesome/6.5.2/LICENSE.txt

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genindex.html

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@@ -435,8 +435,8 @@ <h1>Strukturna biologija<a class="headerlink" href="#strukturna-biologija" title
 <p>Spletna knjiga je v nastajanju in bo kot taka sproti dopolnjena in posodobljena. Priporočam, da si med zaznamke shranite samo osnovni naslov <a class="reference external" href="https://mpavsic.github.io/sbio">https://mpavsic.github.io/sbio</a>, saj se lahko naslovi podstrani v primeru reorganizacije vsebine spremenijo. Če v knjigi najdete napako mi to sporočite preko klika na ikono GitHub <i class="fa-brands fa-github" style="color:Black"></i> na vrhu dotične strani &gt; <code class="docutils literal notranslate"><span class="pre">Suggest</span> <span class="pre">edit</span></code> (predlagajte popravek) ali <code class="docutils literal notranslate"><span class="pre">Open</span> <span class="pre">issue</span></code> (pokomentirajte) – za oboje morete biti vpisani v GitHub, ustvaritev uporabniškega računa je brezplačna.</p>
 </div>
 <hr class="docutils" />
-<p>Pri pripravi logotipa je bila uporabljena modificirana abeceda kristalnih struktur <span id="id1">[<a class="reference internal" href="priloge/reference.html#id7" title="Mark Howarth. Say it with proteins: an alphabet of crystal structures. Nature Structural &amp; Molecular Biology, 22(5):349–349, 2015. doi:10.1038/nsmb.3011.">Howarth, 2015</a>]</span> – zamenjana črka ‘b’ (PDB <a class="reference external" href="https://www.rcsb.org/structure/5IZK">5IZK</a>), dodan <i class="fa fa-heart" style="color:Red"></i> (PDB <a class="reference external" href="https://www.rcsb.org/structure/4MZV">4MZV</a>).</p>
-<p>Vse slike v tej spletni knjigi, razen logotipi institucij in organizacij, so bile pripravljene bodisi kot zaslonske slike ali pa gre za računalniško izrisane vizualizacije (modelov) struktur s programom <a class="reference external" href="https://www.cgl.ucsf.edu/chimerax/">ChimeraX</a> <span id="id2">[<a class="reference internal" href="priloge/reference.html#id8" title="Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng, Gregory S. Couch, Tristan I. Croll, John H. Morris, and Thomas E. Ferrin. Ucsf chimerax: structure visualization for researchers, educators, and developers. Protein Science, 30(1):70-82, 2021. doi:10.1002/pro.3943.">Pettersen <em>et al.</em>, 2021</a>]</span> ali <a class="reference external" href="https://molstar.org/">MolStar</a> <span id="id3">[<a class="reference internal" href="priloge/reference.html#id6" title="David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, and Alexander S Rose. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49(W1):W431–W437, 2021. doi:10.1093/nar/gkab314.">Sehnal <em>et al.</em>, 2021</a>]</span>.</p>
+<p>Pri pripravi logotipa je bila uporabljena modificirana abeceda kristalnih struktur <span id="id1">[<a class="reference internal" href="priloge/reference.html#id9" title="Mark Howarth. Say it with proteins: an alphabet of crystal structures. Nature Structural &amp; Molecular Biology, 22(5):349–349, 2015. doi:10.1038/nsmb.3011.">Howarth, 2015</a>]</span> – zamenjana črka ‘b’ (PDB <a class="reference external" href="https://www.rcsb.org/structure/5IZK">5IZK</a>), dodan <i class="fa fa-heart" style="color:Red"></i> (PDB <a class="reference external" href="https://www.rcsb.org/structure/4MZV">4MZV</a>).</p>
+<p>Vse slike v tej spletni knjigi, razen logotipi institucij in organizacij, so bile pripravljene bodisi kot zaslonske slike ali pa gre za računalniško izrisane vizualizacije (modelov) struktur s programom <a class="reference external" href="https://www.cgl.ucsf.edu/chimerax/">ChimeraX</a> <span id="id2">[<a class="reference internal" href="priloge/reference.html#id10" title="Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng, Gregory S. Couch, Tristan I. Croll, John H. Morris, and Thomas E. Ferrin. Ucsf chimerax: structure visualization for researchers, educators, and developers. Protein Science, 30(1):70-82, 2021. doi:10.1002/pro.3943.">Pettersen <em>et al.</em>, 2021</a>]</span> ali <a class="reference external" href="https://molstar.org/">MolStar</a> <span id="id3">[<a class="reference internal" href="priloge/reference.html#id8" title="David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, and Alexander S Rose. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49(W1):W431–W437, 2021. doi:10.1093/nar/gkab314.">Sehnal <em>et al.</em>, 2021</a>]</span>.</p>
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