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GeoDock

Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.

Try protein docking in Google Colab

Bug reports

If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.

Citing this work

@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}

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Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

www.biorxiv.org/content/10.1101/2023.06.29.547134v1

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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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GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
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Used by
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, '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
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GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
Report repository
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Used by
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
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GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
Report repository
Releases
Packages
Used by
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
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GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
Report repository
Releases
Packages
Used by
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
GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
Report repository
Releases
Packages
Used by
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
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GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
Report repository
Releases
Packages
Used by
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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GeoDock
Official repository for GeoDock: Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
GeoDock is a novel multi-track iterative transformer network designed to address limitations in conventional protein-protein docking algorithms and existing deep learning methods. It is capable of predicting docked structures from separate docking partners, allowing for flexibility at the protein residue level to accommodate conformational changes upon binding. GeoDock attains an average inference speed of under one second on a single GPU, enabling its application in large-scale structure screening.
Try protein docking in Google Colab
Bug reports
If you run into any problems while using GeoDock, please create a Github issue with a description of the problem and the steps to reproduce it.
Citing this work
@article{chu2023flexible,
title={Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer},
author={Chu, Lee-Shin and Ruffolo, Jeffrey A and Harmalkar, Ameya and Gray, Jeffrey J},
journal={Protein Science},
pages={e4862},
year={2023},
publisher={Wiley Online Library}
}
About
Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.
www.biorxiv.org/content/10.1101/2023.06.29.547134v1
Resources
Readme
MIT license
Activity
Custom properties
Stars
102 stars
Watchers
4 watching
Forks
17 forks
Report repository
Releases
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Used by
Contributors
Languages