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    1. PPIS-MDPharmaPPIS-MDPharmaPublic

      Obtain protein-protein interaction stabilizers from molecular dynamics simulation derived pharmacophores

      Python 3

    2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic

      Add NME and ACE chemical groups to protein terminal residues

      Python 8 2

    3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic

      The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

      Python 1

    4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic

      The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

      Python 2

    5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic

      Obtain protein binders from MD generated pharmacophore

      Python

    6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public

      1

    , 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
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;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
ibrahim-mohd (Mohd Ibrahim) · GitHub
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      1. PPIS-MDPharmaPPIS-MDPharmaPublic
        
Obtain protein-protein interaction stabilizers from molecular dynamics simulation derived pharmacophores

        Python
3

      2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic
        
Add NME and ACE chemical groups to protein terminal residues

        Python
8

2

      3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic
        
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

        Python
1

      4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic
        
The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

        Python
2

      5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic
        
Obtain protein binders from MD generated pharmacophore

        Python
      6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public
        
1

      
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
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.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
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document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
ibrahim-mohd (Mohd Ibrahim) · GitHub
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Pinned
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        1. PPIS-MDPharmaPPIS-MDPharmaPublic
          
Obtain protein-protein interaction stabilizers from molecular dynamics simulation derived pharmacophores

          Python
3

        2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic
          
Add NME and ACE chemical groups to protein terminal residues

          Python
8

2

        3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic
          
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

          Python
1

        4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic
          
The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

          Python
2

        5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic
          
Obtain protein binders from MD generated pharmacophore

          Python
        6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public
          
1

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

            Python
3

          2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic
            
Add NME and ACE chemical groups to protein terminal residues

            Python
8

2

          3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic
            
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

            Python
1

          4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic
            
The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

            Python
2

          5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic
            
Obtain protein binders from MD generated pharmacophore

            Python
          6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public
            
1

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

              Python
3

            2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic
              
Add NME and ACE chemical groups to protein terminal residues

              Python
8

2

            3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic
              
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

              Python
1

            4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic
              
The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

              Python
2

            5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic
              
Obtain protein binders from MD generated pharmacophore

              Python
            6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public
              
1

            
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
ibrahim-mohd (Mohd Ibrahim) · GitHub
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Pinned
Loading
              1. PPIS-MDPharmaPPIS-MDPharmaPublic
                
Obtain protein-protein interaction stabilizers from molecular dynamics simulation derived pharmacophores

                Python
3

              2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic
                
Add NME and ACE chemical groups to protein terminal residues

                Python
8

2

              3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic
                
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

                Python
1

              4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic
                
The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

                Python
2

              5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic
                
Obtain protein binders from MD generated pharmacophore

                Python
              6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public
                
1

              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
})();
ibrahim-mohd (Mohd Ibrahim) · GitHub
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Pinned
Loading
                1. PPIS-MDPharmaPPIS-MDPharmaPublic
                  
Obtain protein-protein interaction stabilizers from molecular dynamics simulation derived pharmacophores

                  Python
3

                2. Add-NME-ACE-residues-to-protein-terminal-residuesAdd-NME-ACE-residues-to-protein-terminal-residuesPublic
                  
Add NME and ACE chemical groups to protein terminal residues

                  Python
8

2

                3. undulation-corrected-density-for-lipid-bilayersundulation-corrected-density-for-lipid-bilayersPublic
                  
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes

                  Python
1

                4. Generate-silica-itp-file-GromacsGenerate-silica-itp-file-GromacsPublic
                  
The scripts in this repository creates Gromacs itp files for all-atom simulation of Silica in combination with AMBER force field. For Charmm slight change is required. Refer to the reference in des…

                  Python
2

                5. ProteinBinder-MDPharmaProteinBinder-MDPharmaPublic
                  
Obtain protein binders from MD generated pharmacophore

                  Python
                6. bio-phys/ForceFieldsMC3bio-phys/ForceFieldsMC3Public
                  
1