More ANMD updates

Makefile

@@ -25,7 +25,7 @@ drugui:
 
 pull: clone
 	#git checkout master; git pull origin master
-	cd ProDy; git checkout master; git pull origin master
+	cd ProDy; git checkout main; git pull origin main
 	#cd ProDy; git checkout devel; git pull origin devel
 
 latest: pull
@@ -72,6 +72,12 @@ workdir:
 
 	cp -rf tutorials/cryoem_tutorial/cryoem_tutorial_files/* $(WORKDIR)
 
+	cp -rf tutorials/insty_tutorial/insty_tutorial_files/* $(WORKDIR)
+
+	cp -rf tutorials/watfinder_tutorial/watfinder_tutorial_files/* $(WORKDIR)
+
+	cp -rf tutorials/anmd_tutorial/anmd_tutorial_files/* $(WORKDIR)
+
 #	cp -rf tutorials/saxs_tutorial/saxs_tutorial_files/* $(WORKDIR)
 
 html: link drugui workdir 
@@ -111,3 +117,4 @@ pdf: link
 	make -C tutorials/saxs_tutorial clean copy
 	make -C tutorials/scipion_tutorial clean copy
 	make -C tutorials/watfinder_tutorial  clean copy
+	make -C tutorials/anmd_tutorial  clean copy

_template/anmd.html

@@ -0,0 +1,45 @@
+{% extends "index.html" %}
+{% block body %}
+
+
+      <div class="row">
+        <div class="span12">
+          <div class="span5 pull-right" style="padding-top: 20px">
+            <div class="well">
+              <div id="panel-18-title" class="slide-title"></div>
+              <i class="icon-circle-arrow-right slide-arrow" onclick="nextSlide(18);" title="Next slide"></i>
+              <i class="icon-circle-arrow-left slide-arrow" onclick="prevSlide(18);" title="Previous slide"></i>
+               <div id="panel-18-slide" class="slide-content"></div>
+              <script>showSlide(18, -1);</script>
+            </div>
+          </div>
+
+            <h2>ANMD: All-Atom Sampling of Conformational Space Along ANM Modes of Motion</h2>
+            <p><b>ANMD</b> is an advanced computational approach integrated into ProDy that generates ensembles of realistic all-atom conformations along modes of collective motion predicted by the Anisotropic Network Model (ANM). By coupling ANM with molecular dynamics (MD) energy minimization, ANMD captures large-scale conformational changes responsible for protein function. These functional modes reflect the intrinsic flexibility of proteins and protein-protein complexes, providing critical insights into their dynamic behavior and mechanisms of action.</p>
+
+              <h4>Features</h4>
+              <p>You can use ANMD for
+                <ul>
+                  <li>Sampling all-atom conformers from a folded structure along ANM modes.</li>
+                  <li>Identifying transition intermediates and pathways.</li>
+                  <li>Comparing conformers with experimental data using PCA.</li>
+                  <li>Studying the evolution of protein-protein interactions along functional modes of motion.</li>
+                </ul>
+
+              <p><small>
+              <strong>References</strong><br>
+              Cheng, M.H., Krieger, J.M., Banerjee, A., Xiang, Y., Kaynak, B., Shi, Y., Arditi, M., Bahar, I.
+              <a href="https://doi.org/10.1016/j.isci.2022.103689">Impact of new variants on SARS-CoV-2 infectivity and neutralization</a>, <strong>2022</strong>, <em>iScience</em>, 25(3).
+              <br>
+              Doruker P, Atilgan AR, Bahar I.
+              <a href="https://doi.org/10.1002/1097-0134(20000901)40:4<512::AID-PROT70>3.0.CO;2-V">Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor</a>, <strong>2000</strong>, <em>Proteins</em>, 40:512-524.
+              <br>
+              Atilgan AR, Durrell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I.
+              <a href="https://doi.org/10.1016/S0006-3495(01)76033-X">Anisotropy of fluctuation dynamics of proteins with an elastic network model</a>, <strong>2001</strong>, <em>Biophys. J.</em>, 80:505-515.
+              <br>
+              Eastman, P. et al., <a href="https://doi.org/10.1371/journal.pcbi.1005659">OpenMM 7: Rapid development of high performance algorithms for molecular dynamics</a>, <strong>2017</strong>, <em>PLoS Comput Biol</em>, 13(7):e1005659.
+              </small></p>
+          </div>
+        </div>
+
+{% endblock %}

_template/clustenmd.html

@@ -16,11 +16,12 @@
 
             <h2>ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution</h2>
             <p><b>ClustENMD</b> is a hybrid method that performs unbiased conformational sampling of highly flexible and/or large biomolecular systems 
-              (<a href="https://www.biorxiv.org/content/10.1101/2021.04.16.440182v1">Kaynak et al., 2021</a>; <a href="https://doi.org/10.1021/acs.jctc.6b00319">Kurkcuoglu et al., 2016</a>) 
+              (Kaynak et al., 2021; Kurkcuoglu et al., 2016) 
               with high computational efficiency. The major steps of the algorithm iteratively executed in each generation are: <br>
               (i) deforming each conformer (from previous generation) along random combinations of global ANM modes for generating new conformers, <br>
               (ii) clustering of new conformers to find cluster representatives, and  <br>
-              (iii) performing a short molecular dynamics (MD) simulation for each cluster representative using OpenMM software (<a href="https://doi.org/10.1371/journal.pcbi.1005659">Eastman et al., 2017</a>).</p>
+              (iii) performing a short molecular dynamics (MD) simulation for each cluster representative using OpenMM software 
+              (<a href="https://doi.org/10.1371/journal.pcbi.1005659">Eastman et al., 2017</a>).</p>
 
 
               <h4>Features</h4>
@@ -36,7 +37,7 @@ <h4>Features</h4>
                 </ul>
 
               <p><small>
-              <strong>Reference</strong><br>
+              <strong>References</strong><br>
               Kaynak BT, Zhang S, Bahar I, Doruker P 
               <a href="https://www.biorxiv.org/content/10.1101/2021.04.16.440182v1">ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution</a> 
               <strong>2021</strong> <em>Bionformatics</em> (Accepted).<br>

_template/index.html

@@ -273,7 +273,10 @@
       "WatFinder prediction of water clusters in membrane transporter",
       "WatFinder prediction of water influx in membrane transporter",
       "Scipion-EM-ProDy Ensemble Analysis",
-      "Scipion-EM-ProDy GNM Analysis"
+      "Scipion-EM-ProDy GNM Analysis",
+      "ANMD sampling of mGluR1 NTD along mode 1",
+      "ANMD sampling of mGluR1 NTD along mode 2",
+      "RBD-VH F6 Motion from ANMD"
       );
 
       panelSlides = new Array();
@@ -295,6 +298,7 @@
       panelSlides[15] = new Array(46, 47, 48);
       panelSlides[16] = new Array(49, 50, 51, 52, 53);
       panelSlides[17] = new Array(54, 55);
+      panelSlides[18] = new Array(56, 57, 58);
 
       var slideIndices = [0, 0, 0, 0, 0, 0, 0, 0, 0];
 
@@ -842,6 +846,34 @@
         </p>
       </div>
 
+      <div class="prody-slide" id="slide-56">
+        <div class="slide-image"><img src="../_static/figures/movie1_mGluR_mode1_anmd.gif"/></div>
+        <p></p><p style="font-size: 95%; font-style: italic;">
+          Example output from ANMD analysis of the metabotropic glutamate receptor mGluR1 N-terminal
+          domain showing the generated conformers along mode 1, closing the venus fly trap clamshell.
+        </p>
+      </div>
+
+      <div class="prody-slide" id="slide-57">
+        <div class="slide-image"><img src="../_static/figures/movie2_mGluR_mode2_anmd.gif"/></div>
+        <p></p><p style="font-size: 95%; font-style: italic;">
+          Example output from ANMD analysis of the metabotropic glutamate receptor mGluR1 N-terminal
+          domain showing the generated conformers along mode 1, twisting the venus fly trap clamshell 
+          as in related GABA-B receptors.
+        </p>
+      </div>
+
+      <div class="prody-slide" id="slide-58">
+        <div class="slide-image"><img src="../_static/figures/anmd_fig_allatom.png"/></div>
+        <p></p><p style="font-size: 95%; font-style: italic;">
+          The motion of the Omicron RBD (green) – V<sub>H</sub> F6 (red) complex, generated using ANMD 
+          and sampled along ANM Mode 1 (two shades of cyan, softest mode of motion), enabled quantification of 
+          intrinsic dynamics leading to variability at the interaction interface. The structures are superimposed on 
+          the RBD to highlight variations at the V<sub>H</sub> F6 interface, facilitating an efficient evaluation of 
+          changes in interaction affinity between the RBD and V<sub>H</sub> F6 across Omicron and Wild Type variants.
+        </p>
+      </div>
+
   <div class="container" id="about">
 
 <!-- Logo & Nav
@@ -869,6 +901,7 @@
           <li title="InSty" ><a href="{{ pathto('insty', 1) }}">InSty</a></li>
           <li title="WatFinder" ><a href="{{ pathto('watfinder', 1) }}">WatFinder</a></li>
           <li title="Scipion" ><a href="{{ pathto('scipion', 1) }}">Scipion</a></li>
+          <li title="ANMD" ><a href="{{ pathto('anmd', 1) }}">ANMD</a></li>
           <li title="Downloads"><a href="{{ pathto('downloads', 1) }}">Downloads</a></li>
           <li title="Tutorials"><a href="{{ pathto('tutorials', 1) }}">Tutorials</a></li>
           <li title="Workshops"><a href="{{ pathto('workshop', 1) }}">Workshops</a></li>

_template/insty.html

@@ -42,13 +42,13 @@ <h4>Features</h4>
                   <li>Visualizing the probabilistic occurrence or time evolution of specific interactions</li>
                   <li>Comparing the interactions in different conformations or mutants</li>
                 </ul>
-              <!-- 
+
               <p><small>
               <strong>Reference</strong><br>
-              Mikulska-Ruminska K, Krieger JM, Cao X, Banerjee A, Wu G, Simmerling C, Coutsias EA, Bahar I
+              Mikulska-Ruminska K, Krieger JM, Cao X, Banerjee A, Wu G, Bogetti AT, Zhang F, Simmerling C, Coutsias EA, Bahar I
               InSty: a new module in ProDy for evaluating the interactions and stability of proteins
-              <strong>2024</strong> <em>Bioinformatics</em> 160:104-120.
-              -->
+              <strong>2025</strong> <em>Bioinformatics</em> 169009, https://doi.org/10.1016/j.jmb.2025.169009.
+
           </div>
         </div>
 

_template/tutorials.html

@@ -291,8 +291,8 @@ <h5>CryoDy</h5>
                   <div class="thumbnail text-center" style="height: 310px">
 
                     <img src="../_static/figures/clustenmd_logo_alone.png" style="max-height: 160px">
-                    <h5>ClustENMD and ANMD</h5>
-                    <p class="text-center" style="padding: 0 10 0 10">Learn how to perform conformational sampling using ClustENMD and ANMD. </p>
+                    <h5>ClustENMD</h5>
+                    <p class="text-center" style="padding: 0 10 0 10">Learn how to perform conformational sampling using ClustENMD. </p>
                       <div class="btn-group">
                         <a class="btn btn-primary" href="{{pathto('tutorials/clustenmd_tutorial', 1) }}">Go to Tutorial</a>
                         <!-- <a class="btn btn-primary dropdown-toggle" data-toggle="dropdown" href="#"><span class="caret"></span></a>
@@ -384,6 +384,26 @@ <h5>WatFinder</h5>
                   </div>
                 </li>
 
+                <li class="span4">
+                  <div class="thumbnail text-center" style="height: 310px">
+
+                    <img src="../_static/figures/anmd_fig_allatom.png" style="max-height: 160px">
+                    <h5>ANMD</h5>
+                    <p class="text-center" style="padding: 0 10 0 10">Learn how to perform conformational sampling using ANMD. </p>
+                      <div class="btn-group">
+                        <a class="btn btn-primary" href="{{pathto('tutorials/anmd_tutorial', 1) }}">Go to Tutorial</a>
+                        <!-- <a class="btn btn-primary dropdown-toggle" data-toggle="dropdown" href="#"><span class="caret"></span></a>
+                        <ul class="dropdown-menu">
+                          <li><a href="{{ pathto('tutorials/cryoem_tutorial/EMD-1961.pdb', 1) }}"><i class="icon-download-alt"></i> Input file</a></li>
+                          <li class="divider"></li>
+                          <li><a href="{{ pathto('tutorials/cryoem_tutorial/cryoem_tutorial.tgz', 1) }}"><i class="icon-download-alt"></i> Tutorial files <code>.tgz</code></a></li>
+                          <li><a href="{{ pathto('tutorials/cryoem_tutorial/cryoem_tutorial.zip', 1) }}"><i class="icon-download-alt"></i> Tutorial files <code>.zip</code></a></li>
+                        </ul> -->
+                      </div>
+                  </div>
+                </li>
+
+                <!-- 8TH ROW -->
                 <li class="span4">
                   <div class="thumbnail text-center" style="height: 310px">
                     <img src="{{ pathto('_static/figures/scipion_logo.jpg', 1) }}" style="max-height: 160px">

conf.py

@@ -69,7 +69,8 @@
     'clustenmd/index': 'clustenmd.html',
     'watfinder/index': 'watfinder.html',
     'insty/index': 'insty.html',
-    'scipion/index': 'scipion.html'
+    'scipion/index': 'scipion.html',
+    'anmd/index': 'anmd.html',
 }
 
 html_sidebars = {

contents.rst

@@ -27,6 +27,7 @@ ProDy Documentation
    tutorials/clustenmd_tutorial/index
    tutorials/insty_tutorial/index
    tutorials/watfinder_tutorial/index
+   tutorials/anmd_tutorial/index
    tutorials/scipion_tutorial/index
 
 * :ref:`genindex`

tutorials/anmd_tutorial/Makefile

@@ -0,0 +1 @@
+../template/Makefile

tutorials/anmd_tutorial/acknowledgments.rst

@@ -0,0 +1 @@
+../template/acknowledgments.rst