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<!DOCTYPE html>
<html lang="en">
<head>
<title>Mol*</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
<link rel="icon" href="./favicon.ico" type="image/x-icon">
<link rel="preconnect" href="https://fonts.gstatic.com">
<link href="https://fonts.googleapis.com/css2?family=Source+Sans+Pro:ital,wght@0,400;0,600;1,400;1,600&display=swap"
rel="stylesheet">
<link rel="stylesheet" href="css/normalize.css">
<link rel="stylesheet" href="css/skeleton.css">
<style>
.shadow-img {
box-shadow: 0 0 9px 1px rgba(0, 0, 0, 0.66);
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.founders,
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justify-content: center;
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.founders img {
max-width: 160px;
max-height: 60px;
margin: 0 15px
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max-width: 160px;
width: 100%;
margin: 0 10px;
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opacity: 0.75;
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.examples a:hover {
opacity: 1;
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display: inline-block;
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a:focus+.tooltip .tooltip-info {
display: inline-block;
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a {
text-decoration: none;
}
</style>
</head>
<body>
<div class="container" style="margin-bottom: 20px;">
<div class="row" style="text-align: center; margin: 80px 0 20px 0">
<img style="max-width: 525px; width: 100%;" src="img/molstar-logo.png" />
</div>
<div class="row" style="text-align: center;">
<div class="two columns"> </div>
<div class="eight columns" style="border-top: 1px solid #E0DDD4; padding-top: 20px">
<h5 class="hero-heading">Mol* (<i>/'molstar/</i>) is a modern web-based open-source toolkit for
visualisation and analysis of large-scale molecular data</h5>
</div>
<div class="two columns"> </div>
</div>
<div class="row" style="margin-top: 30px; display: flex;">
<div class="one-half column"
style="display: flex; flex-direction: column; justify-content: center; align-items: center; ">
<a href="viewer" target="_blank" title="Open Mol* Viewer">
<img class="shadow-img" style="max-width: 100%" src="img/viewer.png">
</a>
</div>
<div class="one-half column"
style="display: flex; flex-direction: column; justify-content: center; align-items: center; ">
<a class="button button-primary" href="viewer" style="font-size: 2rem; width: 100%;"
target="_blank">Open Mol* Viewer</a>
<a class="button" href="viewer-docs" style="font-size: 2rem; width: 100%;" target="_blank">Viewer
Documentation</a>
<a class="button" href="https://github.com/molstar/molstar/issues" style="font-size: 2rem; width: 100%;"
target="_blank">Issues & Feedback</a>
<div style="text-align: justify; margin: 5px">
High-performance graphics and data handling of the Mol* Viewer allow users to simultaneously
visualise up to hundreds of (superimposed) protein structures, play molecular dynamics trajectories,
render cell-level models at atomic detail with tens of millions of atoms, or display huge models
obtained by I/HM such as the Nuclear Pore Complex.
</div>
</div>
</div>
<div class="row" style="text-align: center; margin-top: 60px">
<div class="twelve columns">
<h4 class="hero-heading" style="margin-bottom: 40px"><b>Interactive Examples</b></h4>
<div class="examples">
<div class="tooltip">
<a href="https://molstar.org/me/viewer/?example=cellpack-hiv1"
target="_blank"><img alt="HIV in blood serum" src="img/hiv_simple.png" /></a>
<p class="tooltip-info">
CellPack model of enveloped HIV capsid.
<br />
<i>Opens in the <a href="https://molstar.org/me/" target="_blank">Mesoscale Explorer</a></i>
</p>
</div>
<div class="tooltip">
<a href="demos/alpha-orbitals" target="_blank"><img
alt="Alpha orbitals and density of Atorvastatin" src="img/ao.png" /></a>
<p class="tooltip-info">
Alpha orbitals and density of Atorvastatin.
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fzikaem.molx&snapshot-url-type=molx"
target="_blank"><img alt="Zika+EM" src="img/zika.png" /></a>
<p class="tooltip-info">
Zika virus assembly and Cryo-EM density.
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fcytochromes.molx&snapshot-url-type=molx"
target="_blank"><img alt="P-450 Superposition" src="img/cytochromes.png" /></a>
<p class="tooltip-info">
Superposition and validation annotation of P-450 cytochromes.
</p>
</div>
</div>
<div class="examples">
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fgain-md.molx&snapshot-url-type=molx"
target="_blank" title="GAIN domain tethered agonist exposure"><img alt="GAIN domain"
src="img/gain-md.png" /></a>
<p class="tooltip-info">
GAIN domain tethered agonist exposure (<a
href="https://doi.org/10.1016/j.molcel.2020.12.042">doi:10.1016/j.molcel.2020.12.042</a>).
Based on an <a
href="https://twitter.com/ramonguixxa/status/1353767532742766592">animation</a> by Ramon
Guixà-González.
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/me/viewer/?example=petworld-syngap"
target="_blank"><img alt="Petworld synaptic gap" src="img/petworld_synaptic_gap.png" /></a>
<p class="tooltip-info">
Petworld model of the synaptic gap.
<br />
<i>Opens in the <a href="https://molstar.org/me/" target="_blank">Mesoscale Explorer</a></i>
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fnpc.molx&snapshot-url-type=molx"
target="_blank"><img alt="Nuclear Pore Complex" src="img/npc.png" /></a>
<p class="tooltip-info">
IH/M structure of the Nuclear Pore Complex.
</p>
</div>
<div class="tooltip">
<a href="demos/lighting" target="_blank"><img alt="Lighting" src="img/lighting.png" /></a>
<p class="tooltip-info">
Render styles and lighting modes demonstration.
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2F1rb8asm.molx&snapshot-url-type=molx"
target="_blank"><img alt="1RB8 Annotated Assembly" src="img/1rb8.png" /></a>
<p class="tooltip-info">
Annotated assembly of the phiX174 DNA binding protein (PDB id 1RB8).
</p>
</div>
</div>
<div class="examples">
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fvillin-md.molx&snapshot-url-type=molx"
target="_blank" title="Villin trajectory"><img alt="Villin trajectory"
src="img/villin-md.png" /></a>
<p class="tooltip-info">
Villin folding trajectory by Stefan Doerr (<a
href="https://doi.org/10.6084/m9.figshare.12040257.v1">doi:10.6084/m9.figshare.12040257.v1</a>).
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fsars-cov-2_virion.molx&snapshot-url-type=molx"
target="_blank" title="SARS-CoV-2 Virion"><img alt="SARS-CoV-2 Virion"
src="img/sars-cov-2_virion.png" /></a>
<p class="tooltip-info">
SARS-CoV-2 Virion. Coarse-grained model by Alvin Yu et al. (<a
href="https://dx.doi.org/10.1016%2Fj.bpj.2020.10.048">doi:10.1016/j.bpj.2020.10.048</a>).
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fbtub.molx&snapshot-url-type=molx"
target="_blank" title="SARS-CoV-2 Virion"><img alt="BtuB molecules in a lipid bilayer"
src="img/btub.png" /></a>
<p class="tooltip-info">
BtuB molecules in a lipid bilayer. Coarse-grained model by Matthieu Chavent et al. (<a
href="https://dx.doi.org/10.1038/s41467-018-05255-9">doi:10.1038/s41467-018-05255-9</a>).
</p>
</div>
<div class="tooltip">
<a href="https://molstar.org/viewer/?snapshot-url=https%3A%2F%2Fmolstar.org%2Fdemos%2Fstates%2Fmotor-hook.molx&snapshot-url-type=molx"
target="_blank" title="Bacterial flagellar motor-hook complex"><img
alt="bacterial flagellar motor-hook complex" src="img/motor-hook.png" /></a>
<p class="tooltip-info">
Cryo-EM structure of the bacterial flagellar motor-hook complex (<a
href="https://twitter.com/jiaxing_tan_">@Jiaxing_Tan_</a> et al. PDB 7CGO, <a
href="https://dx.doi.org/10.1016/j.cell.2021.03.057">doi:10.1016/j.cell.2021.03.057</a>).
</p>
</div>
</div>
</div>
</div>
<div class="row" style="text-align: justify; margin-top: 50px; padding-top: 40px; border-top: 1px solid #E0DDD4;">
<div class="two columns">
<a href="https://doi.org/10.1093/nar/gkab314">
<img src="img/cover.png" class="shadow-img" alt="NAR Cover Image" style="max-width: 100%; padding: 5px; margin: 3px" />
</a>
</div>
<div class="ten columns">
<a class="button button-primary" href="https://doi.org/10.1093/nar/gkab314"
style="font-size: 2rem; width: 100%;" target="_blank">Read about Mol* in Nucleic Acids Research</a>
<div style="margin: 0 4px">
<b>When using Mol*, please cite:</b><br />
<span style="font-size: smaller;">David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer
Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: <a
href="https://doi.org/10.1093/nar/gkab314">Mol* Viewer: modern web app for 3D visualization and
analysis of large biomolecular structures</a>, <i>Nucleic Acids Research</i>, 2021; <a
href="https://doi.org/10.1093/nar/gkab314">10.1093/nar/gkab31</a>.</span>
</div>
<div style="margin: 0 4px; font-style: italic;">
In memory of Jaroslav Koča.
</div>
</div>
</div>
<svg style="display: none" version="2.0">
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</svg>
<div class="row" style="margin-top: 40px; display: flex;">
<div class="ten columns"
style="display: flex; flex-direction: column; justify-content: center; align-items: center; ">
<a class="button button-primary" href="https://github.com/molstar"
style="font-size: 2rem; width: 100%;">Join Development on GitHub</a>
<a class="button" href="https://molstar.org/docs"
style="font-size: 2rem; width: 100%;">Developer Documentation</a>
<div style="text-align: justify; margin: 5px">
The Mol* toolkit is a comprehensive solution for molecular data delivery, visualization and
analysis that can be embedded into a wide range of 3<sup>rd</sup> party solutions. It includes a
customizable plugin for high quality WebGL based molecular data visualization,
as well as servers for model and experimental (X-ray, Cryo-EM, etc.) data delivery, efficient <a
href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008247"
style="color: #222">BinaryCIF</a> data format support, and other exciting features.
</div>
</div>
<div class="two columns"
style="display: flex; flex-direction: column; justify-content: center; align-items: center; ">
<a href="https://github.com/molstar" title="Join Development on GitHub">
<svg width="120" height="120"><use href="#github-logo" /></svg>
</a>
</div>
</div>
<div class="row" style="margin-top: 40px; padding-top: 40px; text-align: center; border-top: 1px solid #E0DDD4;">
<div class="twelve columns" style="text-align: center">
<h4 class="hero-heading" style="margin-bottom: 40px;"><b>Extensions</b></h4>
</div>
</div>
<div class="row" style="margin-top: 0px; display: flex; font-size: 75%;">
<div class="four columns" style="text-align: center;">
<a href="https://molstar.org/mol-view-spec" class="button button-primary" style="font-size: 2rem; width: 100%;">MolViewSpec</a>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://molstar.org/volumes-and-segmentations" class="button button-primary" style="font-size: 1.75rem; width: 100%;">Volumes and Segmentations</a>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://molstar.org/me" class="button button-primary" style="font-size: 2rem; width: 100%;">Mesoscale Explorer</a>
</div>
</div>
<div class="row" style="margin-top: 10px; display: flex; align-items: center;">
<div class="four columns" style="text-align: center;">
<a href="https://molstar.org/mol-view-spec"><img alt="MolViewSpec Extension" style="max-width: 100%;" class="shadow-img" src="img/ext-mvs.png" /></a>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://molstar.org/volumes-and-segmentations"><img alt="Volumes and Segmentations Extension" style="max-width: 100%;" class="shadow-img" src="img/ext-vol-seg.png" /></a>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://molstar.org/me"><img alt="Mesoscale Explorer" style="max-width: 100%;" class="shadow-img" src="img/ext-me.png" /></a>
</div>
</div>
<div class="row" style="margin-top: 10px; display: flex;">
<div class="four columns" style="text-align: justify;">
<b>MolViewSpec</b> provides a generic mechanism for describing visual scenes or views that are used in molecular visualizations.
It adopts declarative data-driven approach to describe, load, render, and visually deliver molecular structures, along with 3D representations,
coloring schemes, and associated structural, biological, or functional annotations.
</div>
<div class="four columns" style="text-align: justify;">
<b>Volumes and Segmentations</b> extension adds support for large scale volumetric data & their segmentations. Building on the existing Mol* ecosystem, this extension allows seamless
integration of biomolecular data from cellular to atomic scale. It provides the means to visualize large-scale volumetric and segmentation
data from cryo-EM, light miscroscopy, volume-EM, and other imagining experiments together with related 3D model data and biological annotations.
</div>
<div class="four columns" style="text-align: justify;">
The advent of cryo-EM and cryo-ET, coupled with computational modeling,
has enabled the creation of integrative 3D models of viruses, bacteria, and cellular organelles.
Based on these models, the <b>Mesoscale Explorer</b> provides unprecedented access and insight into the molecular fabric of life,
enhancing perception, streamlining exploration, and simplifying visualization of diverse data types, showcasing the intricate details with unparalleled clarity. See the
<a href="https://molstar.org/me/">interactive tours and examples</a>.
</div>
</div>
<div class="row" style="margin-top: 40px; padding-top: 40px; text-align: center; border-top: 1px solid #E0DDD4;">
<div class="twelve columns" style="text-align: center">
<h4 class="hero-heading" style="margin-bottom: 40px;"><b>Community Highlights</b></h4>
</div>
</div>
<div class="row" style="display: flex;">
<div class="four columns" style="text-align: center;">
<a href="https://marketplace.visualstudio.com/items?itemName=ArianJamasb.protein-viewer"><img alt="VSCoding-Sequence" class="shadow-img" style="width: 100%;" src="highlights/vscode.png" /></a>
<div style="text-align: justify; margin-top: 10px;">
<a href="https://marketplace.visualstudio.com/items?itemName=ArianJamasb.protein-viewer">VSCoding-Sequence</a> is an extension for Visual Studio Code that allows for visualization of protein structures and molecular data in the editor.
<a href="https://github.com/molstar/VSCoding-Sequence" style="margin-left: 4px;" title="Join Development on GitHub"><svg width="1em" height="1em"><use href="#github-logo" /></svg></a>
</div>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://reuter-group.github.io/peprmint/pepr2vis/"><img alt="PePr2Vis" class="shadow-img" style="width: 100%;" src="highlights/pepr2vis.png" /></a>
<div style="text-align: justify; margin-top: 10px;">
<a href="https://github.com/reuter-group/peprmint-web">PePr2Vis</a> is a website for the calculation and visualization of protrusions on peripheral membrane proteins.
<a href="https://github.com/reuter-group/peprmint-web" style="margin-left: 4px;" title="Join Development on GitHub"><svg width="1em" height="1em"><use href="#github-logo" /></svg></a>
</div>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://mtzgroup.github.io/molar/"><img alt="MolAR" style="width: 100%;" class="shadow-img" src="highlights/molar.png" /></a>
<div style="text-align: justify; margin-top: 10px;">
<a href="https://mtzgroup.github.io/molar/">MolAR</a> makes chemical structures come to life with augmented reality, see them in a real-world environment.
<a href="https://github.com/sukolsak/molrender3d" style="margin-left: 4px;" title="Join Development on GitHub"><svg width="1em" height="1em"><use href="#github-logo" /></svg></a>
</div>
</div>
<div class="four columns" style="text-align: center;">
<a href="https://alphacharges.ncbr.muni.cz"><img alt="Atomic Charge Calculator II and αCharges" style="width: 100%;" class="shadow-img" src="highlights/acharges.png" /></a>
<div style="text-align: justify; margin-top: 10px;">
<a href="https://acc2.ncbr.muni.cz/">Atomic Charge Calculator II</a> and <a href="https://alphacharges.ncbr.muni.cz">αCharges</a> are web applications for fast computation of partial atomic charges visualized using a custom Mol* extension.
<a href="https://github.com/molstar/molstar/tree/master/src/extensions/sb-ncbr/partial-charges" style="margin-left: 4px;" title="Join Development on GitHub"><svg width="1em" height="1em"><use href="#github-logo" /></svg></a>
</div>
</div>
</div>
<div class="row" style="margin-top: 60px; display: flex;">
<div class="six columns" style="text-align: center;">
<a href="https://pdbe.org"><img alt="PDBe" style="height: 75px" src="img/pdbe_logo.png" /></a>
</div>
<div class="six columns" style="text-align: center;">
<a href="https://rcsb.org"><img alt="PDBe" style="height: 75px" src="img/rcsb_logo.png" /></a>
</div>
</div>
<div class="row" style="margin-top: 20px; display: flex; align-items: flex-start;">
<div class="six columns" style="text-align: center;">
<div style="text-align: justify;">
EMBL-EBI provides an <a href="https://github.com/molstar/pdbe-molstar">open source integration of Mol*</a> used by data resources such
as <a href="https://pdbe.org/">PDBe</a>, <a href="https://pdbe-kb.org/">PDBe-KB</a> and <a href="https://alphafold.ebi.ac.uk/">AlphaFold DB</a>.
This implementation can be embedded as a JS plugin or a Web Component with helper
methods to facilitate programmatic interactions between the web application and the 3D viewer. Its features include a superposition view for overlaying
all observed ligand molecules on representative protein conformations.
</div>
</div>
<div class="six columns" style="text-align: center;">
<div style="text-align: justify;">
<a href="https://www.rcsb.org">RCSB PDB</a> provides an <a href="https://github.com/molstar/rcsb-molstar">open source integration of Mol*</a>
that implements additional functionality, including presets for the visualization of structure alignments and structure motifs such as ligand binding sites,
or the option to interactively add or hide chains and other structural components as showcased by
the <a href="https://www.rcsb.org/3d-sequence/4hhb">3D Protein Feature View</a>.
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</div>
</div>
<div class="row" style="margin-top: 20px; display: flex; align-items: center;">
<div class="six columns" style="text-align: center;">
<a href="https://www.ebi.ac.uk/pdbe/pdbe-kb/"><img alt="PDBe Superposition View" style="max-width: 100%;" class="shadow-img" src="img/pdbe_superposition.png" /></a>
</div>
<div class="six columns" style="text-align: center;">
<a href="https://www.rcsb.org/3d-sequence/4hhb"><img alt="RCSB 3D Protein Feature View" style="max-width: 100%;" class="shadow-img" src="img/rcsb_protein_feature.png" /></a>
</div>
</div>
<div class="row" style="text-align: center; margin-top: 40px">
<div class="twelve columns" style="border-top: 1px solid #E0DDD4; padding-top: 30px">
<h5 class="hero-heading">The project is an open collaboration started by</h5>
<div class="founders">
<a href="https://pdbe.org"><img alt="PDBe" src="img/pdbe_logo.png" /></a>
<a href="https://rcsb.org"><img alt="RCSB" src="img/rcsb_logo.png" /></a>
<a href="https://ceitec.cz"><img alt="CEITEC" src="img/ceitec_logo.jpg" /></a>
<a href="https://www.elixir-czech.cz/services"><img
title="Mol* is a part of services provided by ELIXIR – European research infrastructure for biological information. For other services provided by ELIXIR's Czech Republic Node"
src="img/elixir_logo.png" /></a>
</div>
</div>
</div>
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