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CCPBioSim Docking Workshop

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This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.

This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.

Dependencies:

  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery

If you are using the prepared docker container, all the requirements are installed except ChimeraX.

To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.

If results are published, please cite all of the software that you used. https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html

How to Use

This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.

Pull the container from our repository::

docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::

docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors

Workshop Content Authors:

  • Geoffrey Wells

Contact

Please direct all questions and feedback to Geoffrey Wells

About

A repository containing the build steps for the ccpbiosim workshop on docking

Topics

workshop-materials

Resources

Readme
MIT license
Activity
Custom properties

Stars

6 stars

Watchers

6 watching

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0 forks
Report repository

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
About
A repository containing the build steps for the ccpbiosim workshop on docking
Topics
workshop-materials
Resources
Readme
MIT license
Activity
Custom properties
Stars
6 stars
Watchers
6 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
About
A repository containing the build steps for the ccpbiosim workshop on docking
Topics
workshop-materials
Resources
Readme
MIT license
Activity
Custom properties
Stars
6 stars
Watchers
6 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
About
A repository containing the build steps for the ccpbiosim workshop on docking
Topics
workshop-materials
Resources
Readme
MIT license
Activity
Custom properties
Stars
6 stars
Watchers
6 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
About
A repository containing the build steps for the ccpbiosim workshop on docking
Topics
workshop-materials
Resources
Readme
MIT license
Activity
Custom properties
Stars
6 stars
Watchers
6 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
About
A repository containing the build steps for the ccpbiosim workshop on docking
Topics
workshop-materials
Resources
Readme
MIT license
Activity
Custom properties
Stars
6 stars
Watchers
6 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
About
A repository containing the build steps for the ccpbiosim workshop on docking
Topics
workshop-materials
Resources
Readme
MIT license
Activity
Custom properties
Stars
6 stars
Watchers
6 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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CCPBioSim Docking Workshop
cilatestissuespr
This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This is a repository for a set of Jupyter notebooks to create a workflow for docking ligands to multiple protein receptors and analysing the results.
Dependencies:
  1. Jupyter
  2. ChimeraX (or Chimera, but we recommend the newer ChimeraX)
  3. AutoDock Vina
  4. Vina Split
  5. OpenBabel with Python bindings
  6. OpenDrugDiscovery
If you are using the prepared docker container, all the requirements are installed except ChimeraX.
To install ChimeraX, go to https://www.rbvi.ucsf.edu/chimerax/download.html and download the correct version for your operating system (you will need to click on other releases to find the linux version) and follow the instructions in the notes column on the website. This is for personal non-commercial use.
If results are published, please cite all of the software that you used.
https://vina.scripps.edu/manual/#citationhttps://www.rbvi.ucsf.edu/chimerax/docs/credits.html
How to Use
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/docking-workflow:latest

In our containers we are using the JupyterHub default port 8888, so you should
forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/docking-workflow:latest

Authors
Workshop Content Authors:
  • Geoffrey Wells
Contact
Please direct all questions and feedback to Geoffrey Wells
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A repository containing the build steps for the ccpbiosim workshop on docking
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