archiitecture's picture
Add files using upload-large-folder tool
7ed1ef3 verified
Raw
History Blame Contribute Delete
19.1 kB
<!doctype html><meta charset='utf-8'><title>Initial 8,598 dataset analysis</title>
<style>body{font:15px system-ui;max-width:1100px;margin:32px auto;color:#172638}table{border-collapse:collapse;width:100%;margin:16px 0}th,td{padding:7px;border-bottom:1px solid #dbe3ed;text-align:right}th:first-child,td:first-child{text-align:left}h1{color:#17324d}img{max-width:100%}</style>
<h1>Initial 8,598 dataset diversity analysis</h1>
<p>RCSB structural-cluster annotation is reported only where source-linked PDB entity mapping is available. UniProt annotations are limited to cached exact-sequence matches. Local 3-mer cosine similarity is a sequence-screening proxy, not alignment-derived percent identity.</p><h2>Split, source, and class composition</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>split</th>
<th>dataset_label</th>
<th>source_dataset</th>
<th>proteins</th>
<th>length_median</th>
<th>entropy_median</th>
<th>uniprot_coverage</th>
</tr>
</thead>
<tbody>
<tr>
<td>test</td>
<td>0</td>
<td>ATLAS</td>
<td>30</td>
<td>218.0</td>
<td>4.046595</td>
<td>0.100000</td>
</tr>
<tr>
<td>test</td>
<td>0</td>
<td>Initial sources</td>
<td>142</td>
<td>233.0</td>
<td>4.055927</td>
<td>1.000000</td>
</tr>
<tr>
<td>test</td>
<td>0</td>
<td>PATHpre</td>
<td>295</td>
<td>287.0</td>
<td>4.081072</td>
<td>0.122034</td>
</tr>
<tr>
<td>test</td>
<td>0</td>
<td>Unified completed embeddings</td>
<td>180</td>
<td>279.0</td>
<td>4.095108</td>
<td>0.144444</td>
</tr>
<tr>
<td>test</td>
<td>1</td>
<td>DynamicMPNN additional</td>
<td>164</td>
<td>179.5</td>
<td>4.032586</td>
<td>0.036585</td>
</tr>
<tr>
<td>test</td>
<td>1</td>
<td>DynamicMPNN/RCSB expansion</td>
<td>106</td>
<td>189.5</td>
<td>4.042516</td>
<td>0.009434</td>
</tr>
<tr>
<td>test</td>
<td>1</td>
<td>Initial sources</td>
<td>158</td>
<td>220.0</td>
<td>4.051408</td>
<td>0.069620</td>
</tr>
<tr>
<td>test</td>
<td>1</td>
<td>PATHpre</td>
<td>109</td>
<td>337.0</td>
<td>4.086497</td>
<td>0.073394</td>
</tr>
<tr>
<td>test</td>
<td>1</td>
<td>ProMISE</td>
<td>22</td>
<td>302.5</td>
<td>4.018536</td>
<td>0.000000</td>
</tr>
<tr>
<td>test</td>
<td>1</td>
<td>Unified completed embeddings</td>
<td>84</td>
<td>288.0</td>
<td>4.079219</td>
<td>0.083333</td>
</tr>
<tr>
<td>train</td>
<td>0</td>
<td>ATLAS</td>
<td>168</td>
<td>182.0</td>
<td>4.038397</td>
<td>0.089286</td>
</tr>
<tr>
<td>train</td>
<td>0</td>
<td>Initial sources</td>
<td>698</td>
<td>250.0</td>
<td>4.054581</td>
<td>1.000000</td>
</tr>
<tr>
<td>train</td>
<td>0</td>
<td>PATHpre</td>
<td>1324</td>
<td>284.5</td>
<td>4.080716</td>
<td>0.130665</td>
</tr>
<tr>
<td>train</td>
<td>0</td>
<td>Unified completed embeddings</td>
<td>826</td>
<td>294.0</td>
<td>4.082459</td>
<td>0.129540</td>
</tr>
<tr>
<td>train</td>
<td>1</td>
<td>DynamicMPNN additional</td>
<td>753</td>
<td>185.0</td>
<td>4.050031</td>
<td>0.041169</td>
</tr>
<tr>
<td>train</td>
<td>1</td>
<td>DynamicMPNN/RCSB expansion</td>
<td>484</td>
<td>217.0</td>
<td>4.051139</td>
<td>0.041322</td>
</tr>
<tr>
<td>train</td>
<td>1</td>
<td>Initial sources</td>
<td>700</td>
<td>247.0</td>
<td>4.063712</td>
<td>0.030000</td>
</tr>
<tr>
<td>train</td>
<td>1</td>
<td>PATHpre</td>
<td>607</td>
<td>293.0</td>
<td>4.075814</td>
<td>0.084020</td>
</tr>
<tr>
<td>train</td>
<td>1</td>
<td>ProMISE</td>
<td>109</td>
<td>270.0</td>
<td>4.055181</td>
<td>0.000000</td>
</tr>
<tr>
<td>train</td>
<td>1</td>
<td>Unified completed embeddings</td>
<td>349</td>
<td>288.0</td>
<td>4.069118</td>
<td>0.103152</td>
</tr>
<tr>
<td>val</td>
<td>0</td>
<td>ATLAS</td>
<td>42</td>
<td>185.5</td>
<td>4.013736</td>
<td>0.095238</td>
</tr>
<tr>
<td>val</td>
<td>0</td>
<td>Initial sources</td>
<td>149</td>
<td>228.0</td>
<td>4.043430</td>
<td>1.000000</td>
</tr>
<tr>
<td>val</td>
<td>0</td>
<td>PATHpre</td>
<td>269</td>
<td>295.0</td>
<td>4.078424</td>
<td>0.118959</td>
</tr>
<tr>
<td>val</td>
<td>0</td>
<td>Unified completed embeddings</td>
<td>186</td>
<td>283.0</td>
<td>4.098562</td>
<td>0.134409</td>
</tr>
<tr>
<td>val</td>
<td>1</td>
<td>DynamicMPNN additional</td>
<td>186</td>
<td>186.0</td>
<td>4.035939</td>
<td>0.043011</td>
</tr>
<tr>
<td>val</td>
<td>1</td>
<td>DynamicMPNN/RCSB expansion</td>
<td>98</td>
<td>230.0</td>
<td>4.062461</td>
<td>0.040816</td>
</tr>
<tr>
<td>val</td>
<td>1</td>
<td>Initial sources</td>
<td>141</td>
<td>239.0</td>
<td>4.082550</td>
<td>0.035461</td>
</tr>
<tr>
<td>val</td>
<td>1</td>
<td>PATHpre</td>
<td>119</td>
<td>310.0</td>
<td>4.074416</td>
<td>0.058824</td>
</tr>
<tr>
<td>val</td>
<td>1</td>
<td>ProMISE</td>
<td>24</td>
<td>315.5</td>
<td>4.071043</td>
<td>0.000000</td>
</tr>
<tr>
<td>val</td>
<td>1</td>
<td>Unified completed embeddings</td>
<td>76</td>
<td>294.0</td>
<td>4.063292</td>
<td>0.039474</td>
</tr>
</tbody>
</table><h2>Nearest train-set sequence similarity</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>split</th>
<th>proteins</th>
<th>max_train_similarity</th>
<th>median_train_similarity</th>
<th>high_similarity_pairs</th>
<th>very_high_similarity_pairs</th>
</tr>
</thead>
<tbody>
<tr>
<td>test</td>
<td>1290</td>
<td>0.998683</td>
<td>0.154057</td>
<td>133</td>
<td>103</td>
</tr>
<tr>
<td>val</td>
<td>1290</td>
<td>0.998730</td>
<td>0.155427</td>
<td>120</td>
<td>93</td>
</tr>
</tbody>
</table><h2>Whole-dataset 3-mer cosine clusters at 0.70</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>cross_split</th>
<th>clusters</th>
<th>proteins</th>
</tr>
</thead>
<tbody>
<tr>
<td>False</td>
<td>7708</td>
<td>8019</td>
</tr>
<tr>
<td>True</td>
<td>272</td>
<td>579</td>
</tr>
</tbody>
</table><h2>3-mer cluster summaries by analysis scope</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>scope</th>
<th>proteins</th>
<th>clusters</th>
<th>largest_cluster</th>
<th>multi_protein_clusters</th>
</tr>
</thead>
<tbody>
<tr>
<td>all</td>
<td>8598</td>
<td>7980</td>
<td>13</td>
<td>575</td>
</tr>
<tr>
<td>train_validation</td>
<td>7308</td>
<td>6861</td>
<td>11</td>
<td>418</td>
</tr>
<tr>
<td>test</td>
<td>1290</td>
<td>1275</td>
<td>2</td>
<td>15</td>
</tr>
</tbody>
</table><h2>RCSB 30% structural-cluster coverage</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>split</th>
<th>proteins</th>
<th>rcsb30_coverage</th>
</tr>
</thead>
<tbody>
<tr>
<td>test</td>
<td>1290</td>
<td>0.040310</td>
</tr>
<tr>
<td>train</td>
<td>6018</td>
<td>0.046029</td>
</tr>
<tr>
<td>val</td>
<td>1290</td>
<td>0.051163</td>
</tr>
</tbody>
</table><h2>Mapped RCSB 30% clusters crossing splits</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>cross_split</th>
<th>clusters</th>
<th>proteins</th>
</tr>
</thead>
<tbody>
<tr>
<td>False</td>
<td>359</td>
<td>373</td>
</tr>
<tr>
<td>True</td>
<td>11</td>
<td>22</td>
</tr>
</tbody>
</table><h2>Evidence-backed conformational annotations</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>conformational_evidence_class</th>
<th>observed_state_count_class</th>
<th>size</th>
</tr>
</thead>
<tbody>
<tr>
<td>conditional_switching</td>
<td>unknown</td>
<td>1607</td>
</tr>
<tr>
<td>intrinsic_multistate</td>
<td>unknown</td>
<td>50</td>
</tr>
<tr>
<td>ligand_induced</td>
<td>unknown</td>
<td>55</td>
</tr>
<tr>
<td>multi_state_observed</td>
<td>unknown</td>
<td>1331</td>
</tr>
<tr>
<td>protein_induced</td>
<td>unknown</td>
<td>50</td>
</tr>
<tr>
<td>single_state_observed</td>
<td>1</td>
<td>3080</td>
</tr>
<tr>
<td>unknown</td>
<td>unknown</td>
<td>2425</td>
</tr>
</tbody>
</table><h2>Top UniProt family annotations</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>uniprot_family</th>
<th>size</th>
</tr>
</thead>
<tbody>
<tr>
<td>the globin family</td>
<td>25</td>
</tr>
<tr>
<td>the short-chain dehydrogenases/reductases (SDR) family</td>
<td>11</td>
</tr>
<tr>
<td>the phycobiliprotein family</td>
<td>11</td>
</tr>
<tr>
<td>the MHC class I family</td>
<td>10</td>
</tr>
<tr>
<td>the ATPase alpha/beta chains family</td>
<td>9</td>
</tr>
<tr>
<td>the influenza viruses hemagglutinin family</td>
<td>9</td>
</tr>
<tr>
<td>the archaeal/bacterial/fungal opsin family</td>
<td>9</td>
</tr>
<tr>
<td>the cytochrome P450 family</td>
<td>8</td>
</tr>
<tr>
<td>the polysaccharide monooxygenase AA9 family</td>
<td>6</td>
</tr>
<tr>
<td>the UDP-glycosyltransferase family</td>
<td>6</td>
</tr>
<tr>
<td>the ATPase C chain family</td>
<td>6</td>
</tr>
<tr>
<td>the class-III pyridoxal-phosphate-dependent aminotransferase family</td>
<td>6</td>
</tr>
<tr>
<td>the reaction center PufL/M/PsbA/D family</td>
<td>5</td>
</tr>
<tr>
<td>the archaeal Rpo3/eukaryotic RPB3 RNA polymerase subunit family</td>
<td>5</td>
</tr>
<tr>
<td>the alpha-carbonic anhydrase family</td>
<td>5</td>
</tr>
<tr>
<td>the ferritin family</td>
<td>5</td>
</tr>
<tr>
<td>the class-I pyridoxal-phosphate-dependent aminotransferase family</td>
<td>5</td>
</tr>
<tr>
<td>the mandelate racemase/muconate lactonizing enzyme family</td>
<td>5</td>
</tr>
<tr>
<td>the PNP/UDP phosphorylase family</td>
<td>5</td>
</tr>
<tr>
<td>the AB hydrolase superfamily</td>
<td>4</td>
</tr>
<tr>
<td>the GFP family</td>
<td>4</td>
</tr>
<tr>
<td>the calycin superfamily. Lipocalin family</td>
<td>4</td>
</tr>
<tr>
<td>the NqrDE/RnfAE family</td>
<td>4</td>
</tr>
<tr>
<td>the dihydrofolate reductase family</td>
<td>4</td>
</tr>
<tr>
<td>the NifD/NifK/NifE/NifN family</td>
<td>4</td>
</tr>
<tr>
<td>the Nudix hydrolase family</td>
<td>4</td>
</tr>
<tr>
<td>the glycosyl hydrolase 34 family</td>
<td>4</td>
</tr>
<tr>
<td>the multicopper oxidase family</td>
<td>4</td>
</tr>
<tr>
<td>the glycosyl hydrolase 5 (cellulase A) family</td>
<td>4</td>
</tr>
<tr>
<td>the thiolase-like superfamily. Chalcone/stilbene synthases family</td>
<td>3</td>
</tr>
</tbody>
</table><h2>Amino-acid composition by split</h2><table class="dataframe">
<thead>
<tr style="text-align: right;">
<th>split</th>
<th>A</th>
<th>C</th>
<th>D</th>
<th>E</th>
<th>F</th>
<th>G</th>
<th>H</th>
<th>I</th>
<th>K</th>
<th>L</th>
<th>M</th>
<th>N</th>
<th>P</th>
<th>Q</th>
<th>R</th>
<th>S</th>
<th>T</th>
<th>V</th>
<th>W</th>
<th>Y</th>
</tr>
</thead>
<tbody>
<tr>
<td>test</td>
<td>0.081672</td>
<td>0.013560</td>
<td>0.058221</td>
<td>0.064981</td>
<td>0.041422</td>
<td>0.072544</td>
<td>0.024930</td>
<td>0.056409</td>
<td>0.056946</td>
<td>0.094136</td>
<td>0.023281</td>
<td>0.042767</td>
<td>0.046216</td>
<td>0.036712</td>
<td>0.050196</td>
<td>0.062314</td>
<td>0.054387</td>
<td>0.068665</td>
<td>0.013932</td>
<td>0.034942</td>
</tr>
<tr>
<td>train</td>
<td>0.082188</td>
<td>0.013403</td>
<td>0.057803</td>
<td>0.065399</td>
<td>0.040888</td>
<td>0.073959</td>
<td>0.025210</td>
<td>0.056912</td>
<td>0.056676</td>
<td>0.091967</td>
<td>0.022074</td>
<td>0.042665</td>
<td>0.046767</td>
<td>0.036969</td>
<td>0.050691</td>
<td>0.061621</td>
<td>0.054909</td>
<td>0.069347</td>
<td>0.014051</td>
<td>0.034842</td>
</tr>
<tr>
<td>val</td>
<td>0.082252</td>
<td>0.012960</td>
<td>0.056931</td>
<td>0.065527</td>
<td>0.040476</td>
<td>0.073590</td>
<td>0.025695</td>
<td>0.056600</td>
<td>0.056236</td>
<td>0.092510</td>
<td>0.022827</td>
<td>0.042833</td>
<td>0.046122</td>
<td>0.037414</td>
<td>0.051003</td>
<td>0.062099</td>
<td>0.054992</td>
<td>0.069745</td>
<td>0.013938</td>
<td>0.034828</td>
</tr>
</tbody>
</table><h2>Sequence distributions</h2><h3>Sequence length</h3><svg viewBox='0 0 640 180' role='img'><rect x='0.0' y='166.2' width='19.3' height='13.8' fill='#376996'/><rect x='21.3' y='83.3' width='19.3' height='96.7' fill='#376996'/><rect x='42.7' y='0.2' width='19.3' height='179.8' fill='#376996'/><rect x='64.0' y='0.0' width='19.3' height='180.0' fill='#376996'/><rect x='85.3' y='15.4' width='19.3' height='164.6' fill='#376996'/><rect x='106.7' y='24.8' width='19.3' height='155.2' fill='#376996'/><rect x='128.0' y='26.4' width='19.3' height='153.6' fill='#376996'/><rect x='149.3' y='43.7' width='19.3' height='136.3' fill='#376996'/><rect x='170.7' y='63.0' width='19.3' height='117.0' fill='#376996'/><rect x='192.0' y='84.1' width='19.3' height='95.9' fill='#376996'/><rect x='213.3' y='99.8' width='19.3' height='80.2' fill='#376996'/><rect x='234.7' y='106.5' width='19.3' height='73.5' fill='#376996'/><rect x='256.0' y='121.5' width='19.3' height='58.5' fill='#376996'/><rect x='277.3' y='143.6' width='19.3' height='36.4' fill='#376996'/><rect x='298.7' y='149.5' width='19.3' height='30.5' fill='#376996'/><rect x='320.0' y='159.5' width='19.3' height='20.5' fill='#376996'/><rect x='341.3' y='162.7' width='19.3' height='17.3' fill='#376996'/><rect x='362.7' y='163.9' width='19.3' height='16.1' fill='#376996'/><rect x='384.0' y='162.5' width='19.3' height='17.5' fill='#376996'/><rect x='405.3' y='167.2' width='19.3' height='12.8' fill='#376996'/><rect x='426.7' y='172.1' width='19.3' height='7.9' fill='#376996'/><rect x='448.0' y='170.4' width='19.3' height='9.6' fill='#376996'/><rect x='469.3' y='172.3' width='19.3' height='7.7' fill='#376996'/><rect x='490.7' y='176.7' width='19.3' height='3.3' fill='#376996'/><rect x='512.0' y='175.7' width='19.3' height='4.3' fill='#376996'/><rect x='533.3' y='177.0' width='19.3' height='3.0' fill='#376996'/><rect x='554.7' y='179.8' width='19.3' height='0.2' fill='#376996'/><rect x='576.0' y='179.8' width='19.3' height='0.2' fill='#376996'/><rect x='597.3' y='179.4' width='19.3' height='0.6' fill='#376996'/><rect x='618.7' y='179.8' width='19.3' height='0.2' fill='#376996'/></svg><h3>Sequence entropy</h3><svg viewBox='0 0 640 180' role='img'><rect x='0.0' y='179.8' width='19.3' height='0.2' fill='#376996'/><rect x='21.3' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='42.7' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='64.0' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='85.3' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='106.7' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='128.0' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='149.3' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='170.7' y='179.9' width='19.3' height='0.1' fill='#376996'/><rect x='192.0' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='213.3' y='179.9' width='19.3' height='0.1' fill='#376996'/><rect x='234.7' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='256.0' y='179.7' width='19.3' height='0.3' fill='#376996'/><rect x='277.3' y='179.3' width='19.3' height='0.7' fill='#376996'/><rect x='298.7' y='179.9' width='19.3' height='0.1' fill='#376996'/><rect x='320.0' y='179.9' width='19.3' height='0.1' fill='#376996'/><rect x='341.3' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='362.7' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='384.0' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='405.3' y='179.9' width='19.3' height='0.1' fill='#376996'/><rect x='426.7' y='180.0' width='19.3' height='0.0' fill='#376996'/><rect x='448.0' y='179.9' width='19.3' height='0.1' fill='#376996'/><rect x='469.3' y='179.8' width='19.3' height='0.2' fill='#376996'/><rect x='490.7' y='179.1' width='19.3' height='0.9' fill='#376996'/><rect x='512.0' y='177.5' width='19.3' height='2.5' fill='#376996'/><rect x='533.3' y='174.1' width='19.3' height='5.9' fill='#376996'/><rect x='554.7' y='159.0' width='19.3' height='21.0' fill='#376996'/><rect x='576.0' y='108.0' width='19.3' height='72.0' fill='#376996'/><rect x='597.3' y='0.0' width='19.3' height='180.0' fill='#376996'/><rect x='618.7' y='106.5' width='19.3' height='73.5' fill='#376996'/></svg>