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Yuning Shen commited on
Commit
210c4fb
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1 Parent(s): f192a48

Update conformation tables

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Files changed (6) hide show
  1. data_link/distribution_prediction.csv +8 -21
  2. data_link/multi_state_prediction_apo.csv +7 -18
  3. data_link/multi_state_prediction_bpti.csv +6 -17
  4. data_link/protein_folding.csv +1 -1
  5. data_rank/distribution_prediction.csv +2 -2
  6. data_rank/multi_state_prediction_bpti.csv +2 -2
data_link/distribution_prediction.csv CHANGED
@@ -1,21 +1,8 @@
1
- Model,Pairwise RMSD,RMSF,Pearson r on Pairwise RMSD ↑,Pearson r on Global RMSF ↑,Pearson r on Per target RMSF ↑,RMWD ↓,MD PCA W2 ↓,Joint PCA W2 ↓,PC sim > 0.5% ↑,Weak contacts J ↑,Transient contacts J ↑,Exposed residue J ↑,Exposed MI matrix ρ ↑,CA clash % ↓,CA break % ↓,PepBond break % ↓
2
- MD iid,2.76,1.63,0.96,0.97,0.99,0.67,0.73,0.71,93.9,0.90,0.80,0.93,0.56,0.0,0.0,3.4
3
- MD 2.5ns,1.54,0.98,0.89,0.85,0.85,2.22,1.55,1.89,36.6,0.62,0.45,0.64,0.25,0.0,0.0,3.4
4
- "<a href=""https://github.com/bjing2016/EigenFold"">EigenFold</a>",5.96,NaN,-0.03,NaN,NaN,NaN,2.31,7.96,12.2,0.36,0.19,NaN,NaN,5.6,0.4,NaN
5
- "<a href=""https://github.com/delalamo/af2_conformations"">MSA-depth256</a>",0.83,0.53,0.25,0.34,0.59,3.60,1.79,2.91,29.3,0.30,0.29,0.36,0.06,0.0,0.0,5.5
6
- "<a href=""https://github.com/delalamo/af2_conformations"">MSA-depth64</a>",2.03,1.51,0.25,0.30,0.57,4.00,1.94,3.34,18.3,0.38,0.28,0.40,0.16,0.0,0.0,7.6
7
- "<a href=""https://github.com/delalamo/af2_conformations"">MSA-depth32</a>",5.70,7.96,0.08,0.17,0.53,6.09,2.56,5.70,17.1,0.40,0.24,0.40,0.19,0.1,0.0,11.2
8
- "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-ODE (Tmax=0.1)</a>",1.66,NaN,0.13,NaN,NaN,NaN,2.14,4.39,6.1,0.42,0.18,NaN,NaN,0.0,0.0,12.1
9
- "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-ODE (Tmax=0.3)</a>",3.15,NaN,0.13,NaN,NaN,NaN,2.19,4.80,9.8,0.42,0.17,NaN,NaN,0.0,0.0,13.2
10
- "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-SDE (Tmax=0.1)</a>",4.74,NaN,0.11,NaN,NaN,NaN,2.54,8.82,9.8,0.40,0.13,NaN,NaN,0.1,1.6,21.9
11
- "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-SDE (Tmax=0.3)</a>",7.54,NaN,0.01,NaN,NaN,NaN,3.24,12.28,7.3,0.36,0.13,NaN,NaN,0.2,1.5,20.2
12
- "<a href=""https://github.com/bjing2016/alphaflow"">AlphaFlow-PDB</a>",2.58,1.20,0.27,0.46,0.81,2.97,1.61,2.61,37.8,0.45,0.36,0.50,0.25,0.1,0.0,6.7
13
- "<a href=""https://github.com/bjing2016/alphaflow"">AlphaFlow-MD</a>",2.87,1.63,0.53,0.66,0.85,2.64,1.55,2.29,39.0,0.62,0.41,0.69,0.35,0.0,0.0,22.2
14
- "<a href=""https://github.com/bjing2016/alphaflow"">ESMFlow-PDB</a>",2.99,1.68,0.14,0.27,0.71,4.15,1.87,3.61,28.0,0.42,0.30,0.46,0.21,0.2,0.0,5.1
15
- "<a href=""https://github.com/bjing2016/alphaflow"">ESMFlow-MD</a>",3.33,2.13,0.19,0.30,0.76,3.61,1.66,3.25,25.6,0.55,0.34,0.57,0.29,0.1,0.0,10.9
16
- "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-Open-ClsFree</a>",3.68,2.12,0.39,0.54,0.83,2.91,1.54,2.46,46.3,0.58,0.36,0.60,0.28,0.8,0.0,5.7
17
- "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-Open-PDB</a>",2.89,1.43,0.38,0.51,0.82,2.96,1.59,2.46,34.1,0.50,0.36,0.54,0.25,0.5,0.0,5.6
18
- "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-Open-MD</a>",3.43,2.21,0.59,0.67,0.85,2.75,1.41,2.27,35.4,0.63,0.39,0.65,0.33,0.5,0.0,6.5
19
- "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-ESM-ClsFree</a>",4.04,2.84,0.31,0.43,0.82,3.78,1.73,3.07,37.8,0.57,0.34,0.59,0.23,0.9,0.0,4.3
20
- "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-ESM-PDB</a>",3.42,2.06,0.29,0.40,0.80,3.62,1.68,3.13,34.1,0.50,0.33,0.50,0.24,0.5,0.0,4.0
21
- "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-ESM-MD</a>",3.90,2.79,0.35,0.48,0.82,3.62,1.73,3.00,37.8,0.61,0.36,0.61,0.31,0.4,0.0,4.3
 
1
+ Model,Pairwise RMSD,RMSF,Pearson r on Pairwise RMSD ↑,Pearson r on Global RMSF ↑,Pearson r on Per target RMSF ↑,RMWD ↓,MD PCA W2 ↓,Joint PCA W2 ↓,PC sim > 0.5 (%) ↑,Weak contacts J ↑,Transient contacts J ↑,Exposed residue J ↑,Exposed MI matrix ρ ↑,CA clash (%) ↓,PepBond break (%) ↓
2
+ MD iid,2.76,1.63,0.96,0.97,0.99,0.67,0.73,0.71,93.9,0.90,0.80,0.93,0.56,0.0,3.4
3
+ MD 2.5ns,1.54,0.98,0.89,0.85,0.85,2.22,1.55,1.89,36.6,0.62,0.45,0.64,0.25,0.0,3.4
4
+ "<a href=""https://github.com/bjing2016/EigenFold"">EigenFold</a>",5.96,NaN,-0.03,NaN,NaN,NaN,2.31,7.96,12.2,0.36,0.19,NaN,NaN,5.6,NaN
5
+ "<a href=""https://github.com/delalamo/af2_conformations"">MSA-depth256</a>",0.83,0.53,0.25,0.34,0.59,3.60,1.79,2.91,29.3,0.30,0.29,0.36,0.06,0.0,5.5
6
+ "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-ODE (Tmax=0.1)</a>",1.66,NaN,0.13,NaN,NaN,NaN,2.14,4.39,6.1,0.42,0.18,NaN,NaN,0.0,12.1
7
+ "<a href=""https://github.com/bjing2016/alphaflow"">AlphaFlow-MD</a>",2.87,1.63,0.53,0.66,0.85,2.64,1.55,2.29,39.0,0.62,0.41,0.69,0.35,0.0,22.2
8
+ "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-Open-MD</a>",3.43,2.21,0.59,0.67,0.85,2.75,1.41,2.27,35.4,0.63,0.39,0.65,0.33,0.5,6.5
 
 
 
 
 
 
 
 
 
 
 
 
 
data_link/multi_state_prediction_apo.csv CHANGED
@@ -1,18 +1,7 @@
1
- Model,apo-TM ↑,holo-TM ↑,TMens ↑,Pairwise TM,CA clash (%) ↓,CA break (%) ↓,PepBond break (%) ↓
2
- apo model,1.000,0.790,0.895,NaN,NaN,NaN,NaN
3
- <a href="https://github.com/bjing2016/EigenFold"> EigenFold </a>,0.831,0.864,0.847,0.907,3.6,0.3,NaN
4
- <a href="https://github.com/delalamo/af2_conformations"> MSA-depth256</a>,0.845,0.889,0.867,0.978,0.2,0.0,4.6
5
- <a href="https://github.com/delalamo/af2_conformations"> MSA-depth64</a>,0.844,0.883,0.863,0.950,0.2,0.0,5.7
6
- <a href="https://github.com/delalamo/af2_conformations"> MSA-depth32</a>,0.824,0.857,0.841,0.864,0.2,0.0,8.9
7
- <a href="https://github.com/lujiarui/Str2Str"> Str2Str-ODE (Tmax=0.1)</a>,0.762,0.778,0.770,0.954,0.2,0.0,14.0
8
- <a href="https://github.com/lujiarui/Str2Str"> Str2Str-ODE (Tmax=0.3)</a>,0.766,0.781,0.774,0.872,0.2,0.0,14.7
9
- <a href="https://github.com/lujiarui/Str2Str"> Str2Str-SDE (Tmax=0.1)</a>,0.682,0.693,0.688,0.760,0.2,1.5,22.6
10
- <a href="https://github.com/lujiarui/Str2Str"> Str2Str-SDE (Tmax=0.3)</a>,0.680,0.689,0.684,0.639,0.2,1.4,21.1
11
- <a href="https://github.com/bjing2016/alphaflow">AlphaFlow-PDB</a>,0.855,0.891,0.873,0.924,0.3,0.0,6.6
12
- <a href="https://github.com/bjing2016/alphaflow">AlphaFlow-MD</a>,0.857,0.863,0.860,0.894,0.2,0.0,20.8
13
- <a href="https://github.com/bjing2016/alphaflow">ESMFlow-PDB</a>,0.849,0.882,0.866,0.935,0.3,0.0,4.8
14
- <a href="https://github.com/bjing2016/alphaflow">ESMFlow-MD</a>,0.851,0.864,0.858,0.897,0.1,0.0,10.9
15
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-Open-ClsFree</a> ,0.838,0.879,0.859,0.870,0.8,0.0,5.8
16
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-Open-MD</a> ,0.839,0.874,0.857,0.863,0.4,0.0,6.8
17
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-ESM-ClsFree</a> ,0.837,0.864,0.850,0.846,0.7,0.0,4.6
18
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-ESM-MD</a> ,0.836,0.862,0.849,0.846,0.3,0.0,4.1
 
1
+ Model,apo-TM ↑,holo-TM ↑,TMens ↑,Pairwise TM,CA clash (%) ↓,PepBond break (%) ↓
2
+ apo model,1.000,0.790,0.895,NaN,NaN,NaN
3
+ "<a href=""https://github.com/bjing2016/EigenFold"">EigenFold</a>",0.831,0.864,0.847,0.907,3.6,NaN
4
+ "<a href=""https://github.com/delalamo/af2_conformations"">MSA-depth256</a>",0.845,0.889,0.867,0.978,0.2,4.6
5
+ "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-ODE (Tmax=0.3)</a>",0.766,0.781,0.774,0.872,0.2,14.7
6
+ "<a href=""https://github.com/bjing2016/alphaflow"">AlphaFlow-PDB</a>",0.855,0.891,0.873,0.924,0.3,6.6
7
+ "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-Open-PDB</a>",0.847,0.886,0.867,0.909,0.5,5.5
 
 
 
 
 
 
 
 
 
 
 
data_link/multi_state_prediction_bpti.csv CHANGED
@@ -1,17 +1,6 @@
1
- Model,RMSDens N=10↓,RMSDens N=100↓,RMSDens N=500↓,RMSDens N=1000↓,RMSD Cluster 3 N=10↓,RMSD Cluster 3 N=100↓,RMSD Cluster 3 N=500↓,RMSD Cluster 3 N=1000↓,Pairwise RMSD,CA clash (%)↓,CA break (%)↓,PepBond break (%)↓
2
- <a href="https://github.com/bjing2016/EigenFold"> EigenFold </a>,1.56,1.5,1.47,1.46,2.54,2.48,2.46,2.46,0.85,1.4,4.3,NaN
3
- <a href="https://github.com/delalamo/af2_conformations"> MSA-depth256</a>,1.57,1.54,1.52,1.52,2.51,2.47,2.45,2.45,0.2,0,0,9.2
4
- <a href="https://github.com/delalamo/af2_conformations"> MSA-depth64</a>,1.6,1.54,1.51,1.5,2.48,2.4,2.35,2.33,0.55,0,0,7.9
5
- <a href="https://github.com/delalamo/af2_conformations"> MSA-depth32</a>,1.67,1.53,1.45,1.41,2.39,2.21,1.93,1.87,2.14,0.6,0,10.6
6
- <a href="https://github.com/lujiarui/Str2Str">Str2Str-ODE (Tmax=0.15)</a>,2.36,2.19,2.1,2.08,3.03,2.68,2.6,2.56,1.86,0,0,13.9
7
- <a href="https://github.com/lujiarui/Str2Str">Str2Str-SDE (Tmax=0.15)</a>,2.83,2.48,2.28,2.25,3.42,2.92,2.52,2.48,3.6,0.3,0,16
8
- <a href="https://github.com/bjing2016/alphaflow">AlphaFlow-PDB</a>,1.53,1.45,1.42,1.41,2.48,2.43,2.41,2.4,0.86,0,0,13.2
9
- <a href="https://github.com/bjing2016/alphaflow">AlphaFlow-MD</a>,1.74,1.51,1.45,1.43,2.44,2.32,2.28,2.24,1.26,0,0.1,26.2
10
- <a href="https://github.com/bjing2016/alphaflow">ESMFlow-PDB</a>,1.61,1.49,1.44,1.42,2.47,2.41,2.37,2.35,0.74,0,0,6
11
- <a href="https://github.com/bjing2016/alphaflow">ESMFlow-MD</a>,1.66,1.5,1.41,1.4,2.49,2.29,2.2,2.18,1.17,0,0,14.3
12
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-Open-ClsFree</a>,1.65,1.48,1.41,1.37,2.56,2.3,2.16,2.03,1.77,0.5,0,5.5
13
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-Open-MD</a>,1.64,1.5,1.44,1.42,2.49,2.39,2.32,2.31,1.37,0.2,0,4.6
14
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-ESM-ClsFree</a>,1.58,1.45,1.41,1.39,2.5,2.39,2.35,2.33,1.52,0.5,0,7.5
15
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-ESM-MD</a>,1.61,1.47,1.42,1.4,2.45,2.32,2.26,2.24,1.42,0.1,0,5
16
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-ESM-Energy</a>,1.63,1.47,1.43,1.42,2.55,2.43,2.41,2.4,1.26,0.1,0,7.5
17
- <a href="https://github.com/bytedance/ConfDiff">ConfDiff-ESM-Force</a>,1.58,1.44,1.37,1.36,2.45,2.33,2.23,2.22,1.76,0.1,0,8.9
 
1
+ Model,RMSDens N=10 ↓,RMSDens N=100 ↓,RMSDens N=1000 ↓,RMSD Cluster 3 N=10 ↓,RMSD Cluster 3 N=100 ↓,RMSD Cluster 3 N=1000 ↓,Pairwise RMSD,CA clash (%) ↓,PepBond break (%) ↓
2
+ "<a href=""https://github.com/bjing2016/EigenFold"">EigenFold</a>",1.56,1.50,1.46,2.54,2.48,2.46,0.85,1.4,0.2
3
+ "<a href=""https://github.com/delalamo/af2_conformations"">MSA-depth32</a>",1.66,1.54,1.41,2.43,2.19,1.85,2.14,0.6,10.6
4
+ "<a href=""https://github.com/lujiarui/Str2Str"">Str2Str-SDE (Tmax=0.15)</a>",2.76,2.46,2.26,3.26,2.86,2.55,3.60,0.3,16.0
5
+ "<a href=""https://github.com/bjing2016/alphaflow"">ESMFlow-MD</a>",1.68,1.47,1.39,2.44,2.27,2.18,1.17,0.0,14.3
6
+ "<a href=""https://github.com/bytedance/ConfDiff"">ConfDiff-ESM-Force</a>",1.58,1.43,1.36,2.44,2.35,2.24,1.76,0.1,8.9
 
 
 
 
 
 
 
 
 
 
 
data_link/protein_folding.csv CHANGED
@@ -3,4 +3,4 @@ Model,TM-score ↑,RMSD ↓,GDT-TS ↑,lDDT ↑,CA clash (%) ↓,CA break (%)
3
  <a href="https://github.com/aqlaboratory/openfold/"> OpenFold </a>,0.87,3.21,0.856,0.895,0.4,0,2
4
  <a href="https://github.com/uw-ipd/RoseTTAFold2"> RoseTTAFold2 </a>,0.859,3.52,0.845,0.888,0.3,0.2,5.5
5
  <a href="https://github.com/facebookresearch/esm"> ESMFold </a>,0.847,3.98,0.826,0.87,0.3,0,4.7
6
- <a href="https://github.com/bjing2016/EigenFold"> EigenFold* </a>,0.743,7.65,0.703,0.737,8,0.5,NaN
 
3
  <a href="https://github.com/aqlaboratory/openfold/"> OpenFold </a>,0.87,3.21,0.856,0.895,0.4,0,2
4
  <a href="https://github.com/uw-ipd/RoseTTAFold2"> RoseTTAFold2 </a>,0.859,3.52,0.845,0.888,0.3,0.2,5.5
5
  <a href="https://github.com/facebookresearch/esm"> ESMFold </a>,0.847,3.98,0.826,0.87,0.3,0,4.7
6
+ <a href="https://github.com/bjing2016/EigenFold"> EigenFold </a>,0.743,7.65,0.703,0.737,8,0.5,NaN
data_rank/distribution_prediction.csv CHANGED
@@ -1,2 +1,2 @@
1
- Model,Pairwise RMSD,RMSF,Pearson r on Pairwise RMSD ↑,Pearson r on Global RMSF ↑,Pearson r on Per target RMSF ↑,RMWD ↓,MD PCA W2 ↓,Joint PCA W2 ↓,PC sim > 0.5% ↑,Weak contacts J ↑,Transient contacts J ↑,Exposed residue J ↑,Exposed MI matrix ρ ↑,CA clash % ↓,CA break % ↓,PepBond break % ↓
2
- 0,0,0,-1,-1,-1,1,1,1,-1,-1,-1,-1,-1,1,0,1
 
1
+ Model,Pairwise RMSD,RMSF,Pearson r on Pairwise RMSD ↑,Pearson r on Global RMSF ↑,Pearson r on Per target RMSF ↑,RMWD ↓,MD PCA W2 ↓,Joint PCA W2 ↓,PC sim > 0.5 (%) ↑,Weak contacts J ↑,Transient contacts J ↑,Exposed residue J ↑,Exposed MI matrix ρ ↑,CA clash (%) ↓,PepBond break (%) ↓
2
+ 0,0,0,-1,-1,-1,1,1,1,-1,-1,-1,-1,-1,1,1
data_rank/multi_state_prediction_bpti.csv CHANGED
@@ -1,2 +1,2 @@
1
- Model,RMSDens N=10↓,RMSDens N=100↓,RMSDens N=500↓,RMSDens N=1000↓,RMSD Cluster 3 N=10↓,RMSD Cluster 3 N=100↓,RMSD Cluster 3 N=500↓,RMSD Cluster 3 N=1000↓,Pairwise RMSD,CA clash (%)↓,CA break (%)↓,PepBond break (%)↓
2
- 0,0,0,0,1,0,0,0,1,0,-1,0,-1
 
1
+ Model,RMSDens N=10 ↓,RMSDens N=100 ↓,RMSDens N=1000 ↓,RMSD Cluster 3 N=10 ↓,RMSD Cluster 3 N=100 ↓,RMSD Cluster 3 N=1000 ↓,Pairwise RMSD,CA clash (%) ↓,PepBond break (%) ↓
2
+ 0,1,1,1,1,1,1,0,1,1