Table 4 Prediction error of the RF, ULSTM, BLSTM and CNN-LSTM models, as measured by RMSD metric in Å units. The six transmembrane regions (TM) regions of the APO, FA and PIA simulations for 2rh1 and 3p0g states.

From: GPCR molecular dynamics forecasting using recurrent neural networks

Region

MD-RMSD

RF

USLTM

BLSTM

CNN-LSTM

APO

2rh1

TM1

2.6361

0.2328\(^{**-}\) \({\pm }\) 0.0056

0.1480 \({\pm }\) 0.0080

0.1563 \({\pm }\) 0.0068

0.1518 \({\pm }\) 0.0024

TM2\(^{*+}\)

1.5520

0.1998\(^{**-}\) \({\pm }\) 0.0025

0.1313 \({\pm }\) 0.0075

0.1387 \({\pm }\) 0.0058

0.1350 \({\pm }\) 0.0025

TM3

1.5807

0.2143\(^{**-}\) \({\pm }\) 0.0026

0.1325 \({\pm }\) 0.0077

0.1389 \({\pm }\) 0.0059

0.1364 \({\pm }\) 0.0020

TM4

1.7552

0.2090\(^{**-}\) \({\pm }\) 0.0023

0.1416 \({\pm }\) 0.0068

0.1482 \({\pm }\) 0.0056

0.1472 \({\pm }\) 0.0026

TM5

1.9092

0.2300\(^{**-}\) \({\pm }\) 0.0055

0.1455 \({\pm }\) 0.0084

0.1510 \({\pm }\) 0.0067

0.1501 \({\pm }\) 0.0020

TM6

1.7479

0.5320\(^{**-}\) \({\pm }\) 0.0032

0.1372 \({\pm }\) 0.0153

0.1437 \({\pm }\) 0.0192

0.1412 \({\pm }\) 0.0052

TM7

1.7785

0.2451\(^{**-}\) \({\pm }\) 0.0071

0.1396 \({\pm }\) 0.0072

0.1485 \({\pm }\) 0.0063

0.1428 \({\pm }\) 0.0017

APO

3p0g

TM1

2.1303

0.1921\(^{**-}\) \({\pm }\) 0.0009

0.1480 \({\pm }\) 0.0053

0.1490 \({\pm }\) 0.0039

0.1427 \({\pm }\) 0.0011

TM2\(^{*+}\)

1.6303

0.1694\(^{**-}\) \({\pm }\) 0.0032

0.1340 \({\pm }\) 0.0048

0.1349 \({\pm }\) 0.0040

0.1270 \({\pm }\) 0.0015

TM3

1.5573

0.1585\(^{**-}\) \({\pm }\) 0.0022

0.1370 \({\pm }\) 0.0048

0.1378 \({\pm }\) 0.0035

0.1321 \({\pm }\) 0.0012

TM4

1.6851

0.1874\(^{**-}\) \({\pm }\) 0.0043

0.1433 \({\pm }\) 0.0046

0.1420 \({\pm }\) 0.0045

0.1377 \({\pm }\) 0.0026

TM5

1.8959

0.1693\(^{**-}\) \({\pm }\) 0.0015

0.1514 \({\pm }\) 0.0058

0.1520 \({\pm }\) 0.0040

0.1475 \({\pm }\) 0.0013

TM6

1.7132

0.1730\(^{**-}\) \({\pm }\) 0.0011

0.1517 \({\pm }\) 0.0056

0.1527 \({\pm }\) 0.0042

0.1469 \({\pm }\) 0.0011

TM7

1.6891

0.1726\(^{**-}\) \({\pm }\) 0.0004

0.1680 \({\pm }\) 0.0053

0.1632 \({\pm }\) 0.0040

0.1516 \({\pm }\) 0.0009

FA

2rh1

TM1

2.2130

0.1632\(^{**-}\) \({\pm }\) 0.0014

0.1472 \({\pm }\) 0.0042

0.1488 \({\pm }\) 0.0042

0.1478 \({\pm }\) 0.0045

TM2\(^{*+}\)

1.1630

0.1485\(^{**-}\) \({\pm }\) 0.0018

0.1276 \({\pm }\) 0.0040

0.1279 \({\pm }\) 0.0037

0.1269 \({\pm }\) 0.0044

TM3

1.1557

0.1651\(^{**-}\) \({\pm }\) 0.0034

0.1296 \({\pm }\) 0.0040

0.1261 \({\pm }\) 0.0039

0.1262 \({\pm }\) 0.0044

TM4

1.1685

0.1794\(^{**-}\) \({\pm }\) 0.0027

0.1325 \({\pm }\) 0.0046

0.1331 \({\pm }\) 0.0042

0.1326 \({\pm }\) 0.0041

TM5

1.1896

0.1866\(^{**-}\) \({\pm }\) 0.0013

0.1435 \({\pm }\) 0.0039

0.1449 \({\pm }\) 0.0041

0.1436 \({\pm }\) 0.0044

TM6

1.1713

0.1604\(^{**-}\) \({\pm }\) 0.0021

0.1370 \({\pm }\) 0.0034

0.1380 \({\pm }\) 0.0032

0.1366 \({\pm }\) 0.0042

TM7

1.1689

0.1773\(^{**-}\) \({\pm }\) 0.0031

0.1476 \({\pm }\) 0.0040

0.1442 \({\pm }\) 0.0036

0.1396 \({\pm }\) 0.0040

FA

3p0g

TM1

2.4546

0.1934\(^{**-}\) \({\pm }\) 0.0020

0.1418 \({\pm }\) 0.0054

0.1346 \({\pm }\) 0.0166

0.1355 \({\pm }\) 0.0027

TM2\(^{*+}\)

1.5985

0.1680\(^{**-}\) \({\pm }\) 0.0035

0.1269 \({\pm }\) 0.0046

0.1255 \({\pm }\) 0.0033

0.1205 \({\pm }\) 0.0029

TM3

1.5074

0.1653\(^{**-}\) \({\pm }\) 0.0035

0.1314 \({\pm }\) 0.0047

0.1295 \({\pm }\) 0.0030

0.1248 \({\pm }\) 0.0027

TM4

1.7063

0.1796\(^{**-}\) \({\pm }\) 0.0015

0.1367 \({\pm }\) 0.0047

0.1345 \({\pm }\) 0.0034

0.1312 \({\pm }\) 0.0024

TM5

1.8776

0.1660\(^{**-}\) \({\pm }\) 0.0011

0.1405 \({\pm }\) 0.0052

0.1376 \({\pm }\) 0.0037

0.1337 \({\pm }\) 0.0020

TM6

1.6032

0.1616\(^{**-}\) \({\pm }\) 0.0019

0.1450 \({\pm }\) 0.0053

0.1432 \({\pm }\) 0.0041

0.1390 \({\pm }\) 0.0021

TM7

1.7178

0.1816\(^{**-}\) \({\pm }\) 0.0015

0.1412 \({\pm }\) 0.0052

0.1420 \({\pm }\) 0.0038

0.1357 \({\pm }\) 0.0022

PIA

2rh1

TM1

2.1959

0.1714\(^{**-}\) \({\pm }\) 0.0048

0.1493 \({\pm }\) 0.0216

0.1493 \({\pm }\) 0.0222

0.1434 \({\pm }\) 0.0219

TM2\(^{*+}\)

1.6432

0.1768\(^{**-}\) \({\pm }\) 0.0057

0.1295 \({\pm }\) 0.0156

0.1299 \({\pm }\) 0.0162

0.1248 \({\pm }\) 0.0159

TM3

1.5364

0.1687\(^{**-}\) \({\pm }\) 0.0017

0.1293 \({\pm }\) 0.0214

0.1294 \({\pm }\) 0.0226

0.1246 \({\pm }\) 0.0219

TM4

1.6747

0.1789\(^{**-}\) \({\pm }\) 0.0053

0.1355 \({\pm }\) 0.0136

0.1365 \({\pm }\) 0.0151

0.1326 \({\pm }\) 0.0144

TM5

1.7934

0.1918\(^{**-}\) \({\pm }\) 0.0029

0.1482 \({\pm }\) 0.0342

0.1477 \({\pm }\) 0.0358

0.1427 \({\pm }\) 0.0333

TM6

1.7762

0.1819\(^{**-}\) \({\pm }\) 0.0055

0.1436 \({\pm }\) 0.0259

0.1428 \({\pm }\) 0.0265

0.1380 \({\pm }\) 0.0259

TM7

1.7943

0.1936\(^{**-}\) \({\pm }\) 0.0087

0.1595 \({\pm }\) 0.0106

0.1505 \({\pm }\) 0.0089

0.14314 \({\pm }\) 0.0124

PIA

3p0g

TM1

2.6085

0.1978\(^{**-}\) \({\pm }\) 0.0047

0.1466 \({\pm }\) 0.0074

0.1401 \({\pm }\) 0.0054

0.1417 \({\pm }\) 0.0121

TM2\(^{*+}\)

1.6066

0.1819\(^{**-}\) \({\pm }\) 0.0027

0.1291 \({\pm }\) 0.0071

0.1220 \({\pm }\) 0.0049

0.1244 \({\pm }\) 0.0016

TM3

1.5384

0.1656\(^{**-}\) \({\pm }\) 0.0042

0.1297 \({\pm }\) 0.0069

0.1221\(^{*1}\) \({\pm }\) 0.0048

0.1253 \({\pm }\) 0.0019

TM4

1.6484

0.2159\(^{**-}\) \({\pm }\) 0.0098

0.1338 \({\pm }\) 0.0068

0.1259 \({\pm }\) 0.0049

0.1291 \({\pm }\) 0.0020

TM5

1.8164

0.1845\(^{**-}\) \({\pm }\) 0.0039

0.0068 \({\pm }\) 0.0266

0.1315 \({\pm }\) 0.0053

0.1353 \({\pm }\) 0.0026

TM6

1.5573

0.1838\(^{**-}\) \({\pm }\) 0.0034

0.1457 \({\pm }\) 0.0064

0.1393 \({\pm }\) 0.0050

0.1421 \({\pm }\) 0.0020

TM7

1.7212

0.1919\(^{**-}\) \({\pm }\) 0.0040

0.1482 \({\pm }\) 0.0064

0.1424 \({\pm }\) 0.0050

0.1464 \({\pm }\) 0.0020

Mean

TM1

2.3731

0.1918\(^{**-}\) \({\pm }\) 0.0032

0.1468 \({\pm }\) 0.0086

0.1247 \({\pm }\) 0.0098

0.1438 \({\pm }\) 0.0075

TM2\(^{*+}\)

1.5323

0.1741\(^{**-}\) \({\pm }\) 0.0032

0.1297 \({\pm }\) 0.0073

0.1298 \({\pm }\) 0.0063

0.1264 \({\pm }\) 0.0048

TM3

1.4793

0.1729\(^{**-}\) \({\pm }\) 0.0029

0.1316 \({\pm }\) 0.0083

0.1316 \({\pm }\) 0.0073

0.1292 \({\pm }\) 0.0057

TM4

1.6064

0.1917\(^{**-}\) \({\pm }\) 0.0043

0.1372 \({\pm }\) 0.0068

0.1367 \({\pm }\) 0.0063

0.1351 \({\pm }\) 0.0047

TM5

1.7470

0.1880\(^{**-}\) \({\pm }\) 0.0027

0.1326 \({\pm }\) 0.0140

0.1441 \({\pm }\) 0.0099

0.1421 \({\pm }\) 0.0076

TM6

1.5949

0.2321\(^{**-}\) \({\pm }\) 0.0029

0.1434 \({\pm }\) 0.0103

0.1433 \({\pm }\) 0.0104

0.1406 \({\pm }\) 0.0067

TM7

1.6151

0.1937\(^{**-}\) \({\pm }\) 0.0032

0.1489 \({\pm }\) 0.0056

0.1481 \({\pm }\) 0.0045

0.1432 \({\pm }\) 0.0022

  1. Statistics of significantly worse\(^{(-)}\) and significantly better\(^{(+)}\) differences with p \(< 0.05^{*}\) and p\(< 0.01^{**}\) are included. The symbols in the first column indicate significantly better differences between TM regions, while, in the model results columns, they indicate significantly worse differences between models. The Mean row at the bottom indicates mean errors across regions. Bold values show the minimum error accross regions and models. Symbol \(^{*1}\) refers to no significant differences as compared to TM2.
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