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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>ProVisual - Protein Evidence Workbench</title>
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<link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700;800&family=JetBrains+Mono:wght@500;600&display=swap" rel="stylesheet">
<style>
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--amber:#9a6f00;--ocean:#1a4f6e;
--shadow-s:0 1px 3px rgba(17,17,17,0.06),0 2px 8px rgba(17,17,17,0.04);
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}
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<body>
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<div class="logo">Pv</div>
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<div class="db-tags">
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<div class="search-lbl">UniProt Accession ID</div>
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<svg width="17" height="17" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2.2"><circle cx="11" cy="11" r="8"/><path d="m21 21-4.35-4.35"/></svg>
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</div>
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</section>
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<div class="loader-h">Gathering evidence</div>
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<div class="task" data-t="uniprot"><div class="task-dot"></div><div class="task-name">UniProt - curated annotations and GO terms</div><div class="task-st">Queued</div></div>
<div class="task" data-t="predict"><div class="task-dot"></div><div class="task-name">Kyte-Doolittle - hydrophobicity signal computation</div><div class="task-st">Queued</div></div>
<div class="task" data-t="string"><div class="task-dot"></div><div class="task-name">STRING - protein interaction network</div><div class="task-st">Queued</div></div>
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</div>
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<div id="results"></div>
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<footer><div class="wrap fi"><div>ProVisual - Evidence Integration Workbench</div><div>2026</div></div></footer>
<script>
const KD={A:1.8,R:-4.5,N:-3.5,D:-3.5,C:2.5,Q:-3.5,E:-3.5,G:-0.4,H:-3.2,I:4.5,L:3.8,K:-3.9,M:1.9,F:2.8,P:-1.6,S:-0.8,T:-0.7,W:-0.9,Y:-1.3,V:4.2};
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let S={prot:null,hydro:null,tmPred:[],win:19,thr:1.6,str:null,aiSum:null,chat:[],filt:new Set(),gemKey:''};
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}
function sl(ms){return new Promise(r=>setTimeout(r,ms));}
function parseProt(id,d){
const name=d.proteinDescription?.recommendedName?.fullName?.value||d.proteinDescription?.submittedName?.[0]?.fullName?.value||'Unknown Protein';
const gene=d.genes?.[0]?.geneName?.value||'';
const org=d.organism?.scientificName||'';
const taxon=d.organism?.taxonId||null;
const len=d.sequence?.length||0;
const seq=d.sequence?.value||'';
const fn=d.comments?.find(c=>c.commentType==='FUNCTION');
const rawDesc=fn?.texts?.[0]?.value||'';
const desc=rawDesc.replace(/\s*\(PubMed:[^)]+\)/g,'').replace(/\s*\[PubMed:[^\]]+\]/g,'').trim();
const sc=d.comments?.find(c=>c.commentType==='SUBCELLULAR LOCATION');
const loc=sc?.subcellularLocations?.[0]?.location?.value||null;
const feats=(d.features||[]).map(f=>({type:f.type,desc:f.description||f.type,s:f.location?.start?.value??0,e:f.location?.end?.value??0})).filter(f=>f.e>=f.s&&f.s>0);
const go=extractGO(d);
const ann=new Set();feats.forEach(f=>{for(let i=f.s;i<=f.e;i++)ann.add(i);});
const cov=len>0?Math.round((ann.size/len)*100):0;
return{id,name,gene,org,taxon,len,seq,desc,loc,feats,go,cov};
}
function extractGO(d){
const go={MF:[],BP:[],CC:[]};
(d.uniProtKBCrossReferences||[]).filter(x=>x.database==='GO').forEach(x=>{
const tp=x.properties?.find(p=>p.key==='GoTerm');if(!tp)return;
const t=tp.value;
if(t.startsWith('F:'))go.MF.push({id:x.id,name:t.slice(2)});
else if(t.startsWith('P:'))go.BP.push({id:x.id,name:t.slice(2)});
else if(t.startsWith('C:'))go.CC.push({id:x.id,name:t.slice(2)});
});
return go;
}
function computeHydro(seq,w){
const n=seq.length,p=new Array(n).fill(0),h=Math.floor(w/2);
for(let i=0;i<n;i++){
let s=0,c=0;
for(let j=Math.max(0,i-h);j<=Math.min(n-1,i+h);j++){const v=KD[seq[j]];if(v!==undefined){s+=v;c++;}}
p[i]=c>0?s/c:0;
}
return p;
}
// The sliding window erodes each end of a hydrophobic stretch by up to half its
// width, so a genuine 20-25 residue helix clears the threshold for noticeably
// fewer residues than it actually spans. EGFR's 646-668 helix survives as 13.
const MIN_TM=12;
function predictTM(profile,thr){
const segs=[];let in_=false,st=0;
for(let i=0;i<profile.length;i++){
if(profile[i]>=thr&&!in_){in_=true;st=i;}
else if(profile[i]<thr&&in_){if(i-st>=MIN_TM)segs.push({s:st+1,e:i});in_=false;}
}
if(in_&&profile.length-st>=MIN_TM)segs.push({s:st+1,e:profile.length});
return segs;
}
async function fetchSTRING(g,taxon){
if(!g)return null;
try{
const sp=taxon||'9606';
const r=await fetch(`https://string-db.org/api/json/network?identifiers=${encodeURIComponent(g)}&species=${sp}&limit=15&required_score=400`);
if(!r.ok)return null;
const d=await r.json();
if(!Array.isArray(d)||d.length===0)return null;
const nm=new Map();
d.forEach(e=>{
['preferredName_A','preferredName_B'].forEach(k=>{const n=e[k];if(!nm.has(n))nm.set(n,{name:n,deg:0,scores:[]});});
nm.get(e.preferredName_A).deg++;nm.get(e.preferredName_B).deg++;
nm.get(e.preferredName_A).scores.push(e.score);nm.get(e.preferredName_B).scores.push(e.score);
});
const q=(g||'').toUpperCase();
return{
edges:d.map(e=>({a:e.preferredName_A,b:e.preferredName_B,sc:e.score})),
nodes:Array.from(nm.values()).map(n=>({...n,isQ:n.name.toUpperCase()===q,avg:n.scores.reduce((a,b)=>a+b,0)/n.scores.length}))
};
}catch(e){return null;}
}
async function groq(prompt, sys){
if(!S.gemKey)return null;
try{
const messages=[];
if(sys)messages.push({role:'system',content:sys});
messages.push({role:'user',content:prompt});
const r=await fetch('https://api.groq.com/openai/v1/chat/completions',{
method:'POST',
headers:{'Content-Type':'application/json','Authorization':'Bearer '+S.gemKey},
body:JSON.stringify({model:'llama-3.3-70b-versatile',messages,max_tokens:800,temperature:0.7})
});
if(!r.ok){const e=await r.json();console.error('Groq error',e);return null;}
const d=await r.json();
return d.choices?.[0]?.message?.content?.trim()||null;
}catch(e){console.error(e);return null;}
}
async function fetchAISum(){
const p=S.prot;
const ft=[...new Set(p.feats.map(f=>f.type))].map(t=>`${t}(${p.feats.filter(f=>f.type===t).length})`).join(', ');
const gs=p.go.MF.slice(0,3).map(t=>t.name).join('; ')||'none';
const sp=S.str&&S.str.nodes.length>1?`Partners: ${S.str.nodes.filter(n=>!n.isQ).slice(0,5).map(n=>n.name).join(', ')}.`:'';
const prompt=`You are a concise expert molecular biologist. A student is viewing this protein in a bioinformatics tool. Write a 2-3 sentence plain-language summary explaining what this protein does and why it matters. Be direct, no hedging. Simple language. Do not start with "This protein".
Protein: ${p.name} (${p.id}) Gene: ${p.gene||'?'} Organism: ${p.org} ${p.len} aa Location: ${p.loc||'?'}
Function: ${p.desc.slice(0,500)}
GO MF: ${gs}
${sp}
Only the 2-3 sentence summary. No labels or headings.`;
return await groq(prompt);
}
async function askAI(q){
if(!S.gemKey)return 'Please add your free Groq API key at the top of the page. Get one in 30 seconds at console.groq.com — completely free, no credit card needed.';
const p=S.prot;
const ft=[...new Set(p.feats.map(f=>f.type))].map(t=>`${t}(${p.feats.filter(f=>f.type===t).length})`).join(', ');
const gs=['MF','BP','CC'].map(k=>`${k}: ${p.go[k].slice(0,5).map(t=>t.name).join('; ')||'none'}`).join('. ');
const history=S.chat.map(m=>`${m.r==='user'?'Student':'Assistant'}: ${m.c}`).join('\n');
const sys=`You are a friendly expert molecular biologist helping a bioinformatics student. Answer concisely and directly, 1-3 short paragraphs unless a list is clearly better. Use **bold** for key terms. If asked to find similar proteins, list 3-5 real proteins each with a specific note. If asked to explain a feature, focus on its biological meaning. Never use em dashes. Be direct and clear.
Protein context:
Name: ${p.name} (${p.id}) | Gene: ${p.gene||'?'} | Organism: ${p.org} | ${p.len} aa | Location: ${p.loc||'?'}
Function: ${p.desc.slice(0,600)}
Features: ${ft}
GO: ${gs}
${S.str&&S.str.nodes.length>1?`STRING partners: ${S.str.nodes.filter(n=>!n.isQ).slice(0,10).map(n=>n.name).join(', ')}`:''}
Predicted TM segments: ${S.tmPred.length} | Annotated TM: ${p.feats.filter(f=>f.type==='Transmembrane').length}`;
const fullPrompt=(history?history+'\nStudent: ':'Student: ')+q;
const ans=await groq(fullPrompt,sys);
return ans||'Could not get a response. Check your API key or try again.';
}
const HIGH_FEAT=['Active site','Binding site','Site'];
const MOD_FEAT=['Domain','Transmembrane','Intramembrane','Disulfide bond','Cross-link','Lipidation','Glycosylation','Modified residue'];
const LOW_FEAT=['Region','Motif','Coiled coil','Helix','Beta strand','Turn','Repeat'];
function classifyVariant(v,feats){
const others=feats.filter(f=>f.type!=='Natural variant'&&f.type!=='Mutagenesis');
const overlapping=others.filter(f=>v.s>=f.s&&v.s<=f.e);
if(overlapping.some(f=>HIGH_FEAT.includes(f.type)))return{tier:'high',color:'#b53a10',label:'High impact',overlapping};
if(overlapping.some(f=>MOD_FEAT.includes(f.type)))return{tier:'mod',color:'#c47c00',label:'Moderate impact',overlapping};
if(overlapping.some(f=>LOW_FEAT.includes(f.type)))return{tier:'low',color:'#2c7a4a',label:'Low impact',overlapping};
return{tier:'none',color:'#999999',label:'Non-functional region',overlapping};
}
function variantSec(p){
const variants=p.feats.filter(f=>f.type==='Natural variant');
const classified=variants.map(v=>({...v,...classifyVariant(v,p.feats)}));
const counts={high:0,mod:0,low:0,none:0};
classified.forEach(v=>counts[v.tier]++);
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">03 - Variant Impact</div>
<h2 class="sec-t">Where do <span>natural variants</span> land?</h2>
<p class="sec-sub">Each natural variant from UniProt is classified by what it overlaps. A variant on an active site is functionally dangerous. One in an unstructured region is likely harmless. No existing database shows this distinction visually.</p>
</div>
<div class="src-tags">${srcTag('uniprot','UniProt / Pathology & Biotech / Natural variants',`https://www.uniprot.org/uniprotkb/${p.id}#pathology_and_biotech`)}</div>
</div>
<div class="card card-p">
<div class="var-impact-grid">
<div class="var-impact-card high">
<div class="var-impact-label">High impact</div>
<div class="var-impact-n">${counts.high}</div>
<div class="var-impact-desc">Overlaps active site, binding site, or catalytic residue</div>
</div>
<div class="var-impact-card mod">
<div class="var-impact-label">Moderate impact</div>
<div class="var-impact-n">${counts.mod}</div>
<div class="var-impact-desc">Overlaps domain, transmembrane region, or structural bond</div>
</div>
<div class="var-impact-card low">
<div class="var-impact-label">Low impact</div>
<div class="var-impact-n">${counts.low}</div>
<div class="var-impact-desc">Overlaps structural element like helix, strand, or coil</div>
</div>
<div class="var-impact-card none">
<div class="var-impact-label">Benign region</div>
<div class="var-impact-n">${counts.none}</div>
<div class="var-impact-desc">No overlap with any annotated functional feature</div>
</div>
</div>
<div class="var-track-wrap"><svg class="var-track-svg" id="var-svg"></svg></div>
<div class="var-legend">
<div class="var-leg"><span class="var-leg-dot" style="background:#b53a10"></span>High impact</div>
<div class="var-leg"><span class="var-leg-dot" style="background:#c47c00"></span>Moderate impact</div>
<div class="var-leg"><span class="var-leg-dot" style="background:#2c7a4a"></span>Low impact</div>
<div class="var-leg"><span class="var-leg-dot" style="background:#999"></span>Benign region</div>
</div>
<div class="var-click-hint">Click any variant to ask the AI about its potential biological impact.</div>
</div>
</section>`;}
function drawVariants(p){
const svg=document.getElementById('var-svg');if(!svg)return;
const ns='http://www.w3.org/2000/svg';
const W=920,PL=30,PR=30,BW=W-PL-PR;
const variants=p.feats.filter(f=>f.type==='Natural variant');
const classified=variants.map(v=>({...v,...classifyVariant(v,p.feats)}));
const H=110;
svg.setAttribute('viewBox',`0 0 ${W} ${H}`);svg.setAttribute('height',H);
svg.innerHTML='';
// Background track
svg.appendChild(svgEl(ns,'rect',{x:PL,y:44,width:BW,height:8,fill:'#e8e0d0',rx:4}));
// Axis ticks
for(let i=0;i<=6;i++){
const x=PL+(BW/6)*i;const pos=Math.round((p.len/6)*i);
svg.appendChild(svgEl(ns,'line',{x1:x,y1:52,x2:x,y2:58,stroke:'#bbb','stroke-width':1}));
const t=svgEl(ns,'text',{x:x,y:70,'text-anchor':'middle','font-size':10,fill:'#777','font-family':'JetBrains Mono','font-weight':500});
t.textContent=pos;svg.appendChild(t);
}
// Group variants by position bucket to avoid overlap
const buckets={};
classified.forEach(v=>{
const x=Math.round((v.s/p.len)*BW);
const bucket=Math.round(x/8)*8;
if(!buckets[bucket])buckets[bucket]=[];
buckets[bucket].push(v);
});
// Draw variants as diamonds
Object.entries(buckets).forEach(([bx,bvars])=>{
const x=PL+parseInt(bx);
bvars.forEach((v,bi)=>{
const yOffset=bi*14;
const cy=42-yOffset;
const r=bi===0?7:5;
// Diamond shape
const dx=x,dy=cy;
const d=`M ${dx} ${dy-r} L ${dx+r} ${dy} L ${dx} ${dy+r} L ${dx-r} ${dy} Z`;
const shape=svgEl(ns,'path',{d,fill:v.color,stroke:'white','stroke-width':1.5,style:'cursor:pointer;transition:opacity 0.15s',opacity:0.92});
shape.addEventListener('mouseenter',e=>{
shape.setAttribute('opacity','1');
const overlapNames=v.overlapping.length>0?v.overlapping.map(f=>f.type).filter((t,i,a)=>a.indexOf(t)===i).slice(0,3).join(', '):'no functional feature';
showTT(e,v.label,v.desc&&v.desc!==v.type?v.desc:`Position ${v.s}`,`Overlaps: ${overlapNames}`);
});
shape.addEventListener('mousemove',moveTT);
shape.addEventListener('mouseleave',()=>{shape.setAttribute('opacity','0.92');hideTT();});
shape.addEventListener('click',()=>{
const overlapNames=v.overlapping.length>0?v.overlapping.map(f=>f.type).filter((t,i,a)=>a.indexOf(t)===i).join(', '):'no annotated functional feature';
const q=`This protein has a natural variant at position ${v.s}${v.desc&&v.desc!==v.type?' ('+v.desc+')':''}. It overlaps ${overlapNames}. What is the likely biological impact of a mutation at this position? Could it cause disease?`;
addMsg(q);document.querySelector('.chat-card').scrollIntoView({behavior:'smooth',block:'start'});
});
svg.appendChild(shape);
// Stack indicator for multiple variants in same bucket
if(bi===0&&bvars.length>1){
const badge=svgEl(ns,'text',{x:dx+8,y:dy-8,'font-size':8,fill:v.color,'font-family':'Inter','font-weight':800});
badge.textContent='+'+bvars.length;svg.appendChild(badge);
}
});
});
}
function renderAll(){
const p=S.prot;
const aTM=p.feats.filter(f=>f.type==='Transmembrane');
const ov=concordance(S.tmPred,aTM);const opct=Math.round(ov*100);
const cc=opct>=70?'ok':opct>=30?'':'warn';
const hasTM=S.tmPred.length>0||aTM.length>0;
const hasGO=p.go.MF.length+p.go.BP.length+p.go.CC.length>0;
const hasSTR=!!(S.str&&S.str.nodes.length>1);
const variants=p.feats.filter(f=>f.type==='Natural variant');
const hasVars=variants.length>0;
document.getElementById('results').innerHTML=`
<section class="prot-head">
<div class="prot-badge">${p.id}</div>
<h1 class="prot-name">${esc(p.name)}</h1>
<div class="prot-meta">
${p.gene?`<div><span class="k">Gene</span>${esc(p.gene)}</div>`:''}
${p.org?`<div><span class="k">Organism</span>${esc(p.org)}</div>`:''}
${p.loc?`<div><span class="k">Location</span>${esc(p.loc)}</div>`:''}
</div>
<div class="ai-card" id="ai-card">
<div class="ai-badge"><svg width="12" height="12" viewBox="0 0 24 24" fill="currentColor"><path d="M12 2l2.4 7.6L22 12l-7.6 2.4L12 22l-2.4-7.6L2 12l7.6-2.4L12 2z"/></svg>AI Summary</div>
<div class="ai-loading">${S.gemKey?'Writing summary<span class="dots"></span>':'Add your free Groq API key above to enable AI features.'}</div>
</div>
<div class="stats-row">
<div class="stat"><div class="stat-k">Length</div><div class="stat-v">${p.len.toLocaleString()}<span class="stat-u">aa</span></div><div class="stat-src">UniProt / Sequences / Length</div></div>
<div class="stat"><div class="stat-k">Features</div><div class="stat-v">${p.feats.length}</div><div class="stat-src">UniProt / PTM & Processing / Family & Domains</div></div>
<div class="stat"><div class="stat-k">Coverage</div><div class="stat-v">${p.cov}<span class="stat-u">%</span></div><div class="stat-src">Computed from UniProt feature positions</div></div>
${hasVars?`<div class="stat"><div class="stat-k">Variants</div><div class="stat-v">${variants.length}</div><div class="stat-src">UniProt / Pathology & Biotech / Natural variants</div></div>`:''}
${hasSTR?`<div class="stat"><div class="stat-k">Partners</div><div class="stat-v">${S.str.nodes.length-1}</div><div class="stat-src">STRING / Interaction network / Connected nodes</div></div>`:''}
${hasGO?`<div class="stat"><div class="stat-k">GO Terms</div><div class="stat-v">${p.go.MF.length+p.go.BP.length+p.go.CC.length}</div><div class="stat-src">UniProt / Function / GO annotations</div></div>`:''}
</div>
</section>
${chatSec(p)}
${stripSec(p)}
${hasVars?variantSec(p):''}
${radarSec(p)}
${hasTM?tmSec(opct,cc,aTM):''}
${hasSTR?netSec():''}
${hasGO?goSec(p):''}
${aaSec()}
${resSec(p)}
`;
document.getElementById('results').classList.add('on');
setupFilters();drawStrip();
if(hasVars)drawVariants(p);
drawRadar();
if(hasTM){drawHydro();drawOverlay();}
if(hasSTR)drawNet();
drawAA();
setupChat();
}
function renderAICard(){
const el=document.getElementById('ai-card');if(!el)return;
if(S.aiSum){
el.innerHTML=`<div class="ai-badge"><svg width="12" height="12" viewBox="0 0 24 24" fill="currentColor"><path d="M12 2l2.4 7.6L22 12l-7.6 2.4L12 22l-2.4-7.6L2 12l7.6-2.4L12 2z"/></svg>AI Summary</div><div class="ai-text">${esc(S.aiSum)}</div>`;
}else{
el.innerHTML=`<div class="ai-badge">UniProt Description</div><div class="ai-text" style="font-size:1.05rem;font-family:Inter;">${esc((S.prot.desc||'No description available.').slice(0,440))}</div>`;
}
}
const EXT_ICON=`<svg viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2.5"><path d="M18 13v6a2 2 0 01-2 2H5a2 2 0 01-2-2V8a2 2 0 012-2h6"/><polyline points="15 3 21 3 21 9"/><line x1="10" y1="14" x2="21" y2="3"/></svg>`;
function srcTag(cls,label,url){return `<a class="src-tag ${cls}" href="${url}" target="_blank">${EXT_ICON}${label}</a>`;}
function chatSec(p){return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">01 - AI Assistant</div>
<h2 class="sec-t">Ask anything about <span>${esc(p.name.split(' ').slice(0,3).join(' '))}</span></h2>
<p class="sec-sub">Ask questions in plain English, find similar proteins, or click any feature in the strip below to have it explained.</p>
</div>
<div class="src-tags">${srcTag('groq','Groq / Llama 3.3 70B (free)','https://console.groq.com')}</div>
</div>
<div class="chat-card">
<div class="chat-hd">
<div class="chat-icon"><svg width="16" height="16" viewBox="0 0 24 24" fill="currentColor"><path d="M12 2l2.4 7.6L22 12l-7.6 2.4L12 22l-2.4-7.6L2 12l7.6-2.4L12 2z"/></svg></div>
<div><div class="chat-title">Ask about <span>${esc(p.name.split(' ').slice(0,2).join(' '))}</span></div>
<div class="chat-sub">Powered by Groq + Llama 3.3 70B (free) - uses everything fetched from UniProt, STRING, and Gene Ontology</div></div>
</div>
<div class="suggestions">
<div class="sug" onclick="suggest('What does this protein actually do in the cell?')">What does it do?</div>
<div class="sug" onclick="suggest('Find 5 proteins with similar function and explain key differences')">Find similar proteins</div>
<div class="sug" onclick="suggest('What is the most functionally important region in this protein and why?')">Most important region</div>
<div class="sug" onclick="suggest('Is this protein linked to any human diseases?')">Disease relevance</div>
<div class="sug" onclick="suggest('What pathways or complexes does this protein participate in?')">Pathways</div>
</div>
<div class="chat-input-row">
<input class="chat-input" id="chatIn" placeholder="Ask anything..."/>
<button class="btn btn-primary" onclick="doChat()"><svg width="15" height="15" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2.5"><path d="M22 2L11 13M22 2l-7 20-4-9-9-4 20-7z"/></svg></button>
</div>
<div class="chat-msgs" id="chatMsgs"></div>
</div>
</section>`;}
function stripSec(p){
const types=[...new Set(p.feats.map(f=>f.type))].sort((a,b)=>FORDER.indexOf(a)-FORDER.indexOf(b));
S.filt=new Set(types);
const cts={};p.feats.forEach(f=>{cts[f.type]=(cts[f.type]||0)+1;});
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">02 - Structure</div>
<h2 class="sec-t"><span>Features</span> along the sequence</h2>
<p class="sec-sub">Every annotated region rendered spatially. Click any feature block to ask the AI what it means biologically.</p>
</div>
<div class="src-tags">
${srcTag('uniprot','UniProt / PTM & Processing',`https://www.uniprot.org/uniprotkb/${p.id}#ptm_processing`)}
${srcTag('uniprot','UniProt / Family & Domains',`https://www.uniprot.org/uniprotkb/${p.id}#family_domains`)}
</div>
</div>
<div class="card card-p">
<div style="font-size:0.8rem;font-weight:700;color:var(--ink3);text-transform:uppercase;letter-spacing:0.08em;margin-bottom:12px;">Feature landscape - ${p.len} residues</div>
<div class="strip-wrap"><svg class="strip-svg" id="strip-svg"></svg></div>
<div class="fbar" id="fbar">
${types.map(t=>{const c=FC[t]||'#777';return `<label class="fchip on" data-type="${t}"><span class="fdot" style="background:${c}"></span>${t} <span class="fct">${cts[t]}</span></label>`;}).join('')}
</div>
</div>
</section>`;}
function radarSec(p){
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">04 - Protein Profile</div>
<h2 class="sec-t">Protein <span>fingerprint</span></h2>
<p class="sec-sub">A radar chart showing six key dimensions of this protein - computed from the fetched data. Each axis shows how this protein scores relative to typical values.</p>
</div>
<div class="src-tags">
${srcTag('uniprot','UniProt / entry',`https://www.uniprot.org/uniprotkb/${p.id}`)}
${srcTag('string','STRING / network',`https://string-db.org/cgi/network?identifiers=${encodeURIComponent(p.gene||p.id)}&species=${p.taxon||9606}`)}
${srcTag('computed','Computed / Kyte-Doolittle','https://en.wikipedia.org/wiki/Hydrophilicity_plot')}
</div>
</div>
<div class="card card-p">
<div class="radar-wrap">
<canvas id="radar-canvas" width="280" height="280" class="radar-svg"></canvas>
<div class="radar-legend" id="radar-legend"></div>
</div>
</div>
</section>`;}
function tmSec(opct,cc,aTM){
const p=S.prot;
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">05 - Sequence Signal</div>
<h2 class="sec-t">Does the sequence <span>agree</span> with annotation?</h2>
<p class="sec-sub">Kyte-Doolittle hydrophobicity computed from the raw sequence, then compared against UniProt curated transmembrane regions. Adjust window and threshold to explore how the prediction changes.</p>
</div>
<div class="src-tags">
${srcTag('uniprot','UniProt / PTM & Processing / Transmembrane',`https://www.uniprot.org/uniprotkb/${p.id}#ptm_processing`)}
${srcTag('computed','Computed / Kyte-Doolittle sliding window','https://en.wikipedia.org/wiki/Hydrophilicity_plot')}
</div>
</div>
<div class="card card-p" style="margin-bottom:16px;">
<div class="tm-ctrl">
<div class="sw"><div class="sw-lbl"><span>Window size</span><span class="sv" id="winv">${S.win} residues</span></div><input type="range" min="5" max="31" step="2" value="${S.win}" class="slider" oninput="updTM(this.value,null)"/></div>
<div class="sw"><div class="sw-lbl"><span>Threshold</span><span class="sv" id="thrv">${S.thr.toFixed(2)}</span></div><input type="range" min="0.5" max="2.5" step="0.05" value="${S.thr}" class="slider" oninput="updTM(null,this.value)"/></div>
</div>
<svg class="hydro-svg" id="hydro-svg"></svg>
</div>
<div class="main-grid">
<div class="card card-p">
<div style="font-size:0.8rem;font-weight:700;color:var(--ink3);text-transform:uppercase;letter-spacing:0.08em;margin-bottom:12px;">Overlay - Annotated vs Predicted</div>
<svg class="overlay-svg" id="overlay-svg"></svg>
<div class="explain" id="tm-exp" style="display:none;"><div class="explain-h">Why was this predicted?</div><div id="exp-content"></div></div>
<div style="font-size:0.78rem;color:var(--ink3);margin-top:11px;font-weight:500;">Click a predicted segment to see why it was flagged.</div>
</div>
<div class="side-col">
<div class="metric"><div class="metric-k">Agreement</div><div class="metric-v ${cc}" id="concord-v">${opct}%</div><div class="metric-s">Residue overlap between predicted and annotated transmembrane positions.</div></div>
<div class="metric"><div class="metric-k">Predicted</div><div class="metric-v" id="pred-ct">${S.tmPred.length}</div><div class="metric-s">Hydrophobic segments found by the sliding window.</div></div>
<div class="metric"><div class="metric-k">Annotated</div><div class="metric-v">${aTM.length}</div><div class="metric-s">Curated transmembrane regions in UniProt.</div></div>
</div>
</div>
</section>`;}
function netSec(){
const o=S.str.nodes.filter(n=>!n.isQ);
const hub=o.length>0?o.reduce((a,b)=>a.deg>b.deg?a:b,o[0]):null;
const p=S.prot;
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">06 - Context</div>
<h2 class="sec-t">Who does it <span>work with?</span></h2>
<p class="sec-sub">Interaction partners from STRING. Node size reflects degree within this neighbourhood. Click any partner to ask the AI about that specific relationship.</p>
</div>
<div class="src-tags">${srcTag('string','STRING / Interaction network',`https://string-db.org/cgi/network?identifiers=${encodeURIComponent(p.gene||p.id)}&species=${p.taxon||9606}`)}</div>
</div>
<div class="main-grid">
<div class="net-viz"><svg class="net-svg" id="net-svg"></svg></div>
<div class="side-col">
<div class="node-info" id="nodeInfo"><div class="ni-h">Hover a node</div><div style="color:var(--ink3);font-size:0.82rem;line-height:1.5;margin-top:4px;font-weight:500;">Hover or click any protein to see its role and connection strength.</div></div>
<div class="card card-p" style="padding:16px 18px;">
<div class="metric-k">Neighbourhood</div>
<div style="display:flex;flex-direction:column;gap:8px;margin-top:8px;font-size:0.87rem;">
<div style="display:flex;justify-content:space-between;"><span style="color:var(--ink3);font-weight:600;">Partners</span><strong>${o.length}</strong></div>
<div style="display:flex;justify-content:space-between;"><span style="color:var(--ink3);font-weight:600;">Edges</span><strong>${S.str.edges.length}</strong></div>
${hub?`<div style="display:flex;justify-content:space-between;"><span style="color:var(--ink3);font-weight:600;">Top hub</span><strong>${esc(hub.name)}</strong></div>`:''}
</div>
</div>
</div>
</div>
</section>`;}
function goSec(p){return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">07 - Function</div>
<h2 class="sec-t">Gene Ontology <span>assignments</span></h2>
<p class="sec-sub">Three aspects of GO - what the protein does molecularly, which biological processes it participates in, and where in the cell it operates.</p>
</div>
<div class="src-tags">${srcTag('uniprot','UniProt / Function / GO annotations',`https://www.uniprot.org/uniprotkb/${p.id}#function`)}</div>
</div>
<div class="go-grid">
<div class="go-col"><div class="go-col-hd"><span class="go-chip mf">MF</span><span class="go-col-t">Molecular function</span></div>${p.go.MF.length===0?'<div style="color:var(--ink3);font-size:0.85rem;font-weight:500;">No terms assigned.</div>':p.go.MF.slice(0,8).map(t=>`<div class="goterm"><div class="goterm-n">${esc(t.name)}</div><div class="goterm-id">${t.id}</div></div>`).join('')}</div>
<div class="go-col"><div class="go-col-hd"><span class="go-chip bp">BP</span><span class="go-col-t">Biological process</span></div>${p.go.BP.length===0?'<div style="color:var(--ink3);font-size:0.85rem;font-weight:500;">No terms assigned.</div>':p.go.BP.slice(0,8).map(t=>`<div class="goterm"><div class="goterm-n">${esc(t.name)}</div><div class="goterm-id">${t.id}</div></div>`).join('')}</div>
<div class="go-col"><div class="go-col-hd"><span class="go-chip cc">CC</span><span class="go-col-t">Cellular component</span></div>${p.go.CC.length===0?'<div style="color:var(--ink3);font-size:0.85rem;font-weight:500;">No terms assigned.</div>':p.go.CC.slice(0,8).map(t=>`<div class="goterm"><div class="goterm-n">${esc(t.name)}</div><div class="goterm-id">${t.id}</div></div>`).join('')}</div>
</div>
</section>`;}
function aaSec(){
const p=S.prot;
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">08 - Composition</div>
<h2 class="sec-t">Amino acid <span>distribution</span></h2>
<p class="sec-sub">Colored by physicochemical class - the same groupings behind BLOSUM substitution matrices.</p>
</div>
<div class="src-tags">${srcTag('uniprot','UniProt / Sequences',`https://www.uniprot.org/uniprotkb/${p.id}#sequences`)}</div>
</div>
<div class="card card-p">
<div class="aa-bars" id="aa-bars"></div>
<div class="aa-legend">
<div class="aa-leg"><span class="aa-dot" style="background:${ClsCol.h}"></span>Nonpolar / hydrophobic</div>
<div class="aa-leg"><span class="aa-dot" style="background:${ClsCol.n}"></span>Polar uncharged</div>
<div class="aa-leg"><span class="aa-dot" style="background:${ClsCol.p}"></span>Positively charged</div>
<div class="aa-leg"><span class="aa-dot" style="background:${ClsCol.g}"></span>Negatively charged</div>
<div class="aa-leg"><span class="aa-dot" style="background:${ClsCol.s}"></span>Special (G, P)</div>
</div>
</div>
</section>`;}
function resSec(p){
const fa=`>${p.id}\n${p.seq.match(/.{1,60}/g)?.join('\n')||p.seq}`;
return `
<section class="section">
<div class="sec-hd">
<div>
<div class="sec-num">09 - Go Deeper</div>
<h2 class="sec-t">Continue <span>investigating</span></h2>
<p class="sec-sub">Pivot to the primary databases for detail ProVisual does not show.</p>
</div>
<div class="src-tags">
${srcTag('uniprot','UniProt',`https://www.uniprot.org/uniprotkb/${p.id}`)}
${srcTag('ncbi','NCBI BLAST','https://blast.ncbi.nlm.nih.gov')}
${srcTag('string','STRING',`https://string-db.org`)}
${p.gene?srcTag('kegg','KEGG',`https://www.genome.jp/kegg/`):''}
</div>
</div>
<div class="res-grid">
<a class="res-a" href="https://www.uniprot.org/uniprotkb/${p.id}" target="_blank"><div class="res-db">UniProt</div><div class="res-title">Full entry</div><div class="res-desc">All annotations, publications, and cross-references for ${p.id}.</div><div class="res-arr">Go</div></a>
<a class="res-a" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&QUERY=${encodeURIComponent(fa)}" target="_blank"><div class="res-db">NCBI BLAST</div><div class="res-title">Find homologs</div><div class="res-desc">Submit this sequence to BLASTp for a homology search.</div><div class="res-arr">Go</div></a>
<a class="res-a" href="https://string-db.org/cgi/network?identifiers=${encodeURIComponent(p.gene||p.id)}&species=${p.taxon||9606}" target="_blank"><div class="res-db">STRING</div><div class="res-title">Full network</div><div class="res-desc">Expanded interaction network with all evidence channels.</div><div class="res-arr">Go</div></a>
${p.gene?`<a class="res-a" href="https://www.genome.jp/kegg-bin/search_pathway_text?map=map&keyword=${encodeURIComponent(p.gene)}&mode=1" target="_blank"><div class="res-db">KEGG</div><div class="res-title">Pathways</div><div class="res-desc">Metabolic and signalling pathways containing ${p.gene}.</div><div class="res-arr">Go</div></a>`:''}
</div>
</section>`;}
function setupChat(){
const i=document.getElementById('chatIn');if(!i)return;
i.addEventListener('keydown',e=>{if(e.key==='Enter'&&!e.shiftKey){e.preventDefault();doChat();}});
}
function suggest(q){addMsg(q);}
async function doChat(){const i=document.getElementById('chatIn');const q=i.value.trim();if(!q)return;i.value='';await addMsg(q);}
async function addMsg(q){
const msgs=document.getElementById('chatMsgs');
const u=document.createElement('div');u.className='cmsg user';u.textContent=q;msgs.appendChild(u);
const a=document.createElement('div');a.className='cmsg ai';
a.innerHTML=`<div class="ai-lbl"><svg width="11" height="11" viewBox="0 0 24 24" fill="currentColor"><path d="M12 2l2.4 7.6L22 12l-7.6 2.4L12 22l-2.4-7.6L2 12l7.6-2.4L12 2z"/></svg>Llama 3</div><div class="ai-body thinking">Thinking<span class="dots"></span></div>`;
msgs.appendChild(a);a.scrollIntoView({behavior:'smooth',block:'nearest'});
const ans=await askAI(q);
S.chat.push({r:'user',c:q});S.chat.push({r:'assistant',c:ans});
a.querySelector('.ai-body').classList.remove('thinking');
a.querySelector('.ai-body').innerHTML=fmt(ans);
a.scrollIntoView({behavior:'smooth',block:'nearest'});
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function fmt(t){
if(t.includes('<p>')||t.includes('<strong>'))return t;
let h=t.replace(/\*\*(.+?)\*\*/g,'<strong>$1</strong>').replace(/\*(.+?)\*/g,'$1');
return h.split(/\n\n+/).map(p=>{
const ls=p.split('\n');
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