Table 1.
Summary of All Protein and Nucleic Acid Systems Investigated with HDBSCAN and Amorim–Hennig Methodsa
| biopolymer | atoms | frames | HBDSCAN
|
Amorim–Hennig
|
||||
|---|---|---|---|---|---|---|---|---|
| memory (kb) | time ([hh]:mm:ss) | result | memory (kb) | time ([hh]:mm:ss) | result | |||
| MutSα in presence of cisplatinated DNA | 1829 | 5 000 | 1049724 | 04:41 | 1 state per trajectory | 16307300 | 33:28 | 3 stable states |
| MutSα in presence of fluoridated DNA | 1829 | 5 000 | 3080308 | 27:40 | 1 state per trajectory | 122362552 | 03:45:46 | 1 state per trajectory |
| MutSα in presence of mismatched DNA | 1829 | 5 000 | 446560 | 03:32 | 1 state per trajectory | 16755112 | 55:12 | 3 stable, 1 transient state |
| NEMO-CYNZN | 28 | 98 304 | 1017248 | 15:46 | 1 stable state, 75% of frames | 7027188 | 34:22 | 4 stable states |
| NEMO-CYS | 28 | 98 304 | 2380156 | 05:02:34 | 42% noise, 2.4% most populated state | 64461880 | 120:00:00 | 2 frequently switching states |
| SufC108–116 | 246 | 1 000 | ** | 00:33 | 30% noise, 49% most populated state | 2597720 | 04:37 | 4 stable, 3 transient states |
| SufCD108–116 | 671 | 701 | ** | 00:12 | 18% noise, 44% most populated state | 146248 | 02:05 | 2 stable states |
| villin headpiece | 64 | 30 605 | 1570492 | 34:20 | stable segments with periods of instability | 33896452 | 04:25:57 | stages of folding |
| F10 (CaCl2) | 197 | 16 000 | 204536 | 04:15 | 1 dominant state per trajectory | 10567036 | 15:55 | 1 dominant state per trajectory |
| F10 (NaCl) | 197 | 16 000 | 1049908 | 05:38 | 74% noise, 1.4% most populated state | 8715716 | 33:48 | 2 frequently switching states |
| F10 (MgCl2) | 197 | 1 000 | ** | 00:10 | 64% noise, 6.2% most populated state | 2608468 | 09:18 | 5 frequently switching states |
| thrombin aptamer | 315 | 25 770 | 1256036 | 14:14 | 27% noise, 17% most populated state | 18838956 | 01:42:49 | various levels of compactness |
| thrombin (KCl) | 295 | 5 000 | 139136 | 01:08 | 29% noise, 14% most populated state | 7904572 | 01:13:29 | 2 stable, 1 transient state(s) |
| thrombin (NaCl) | 295 | 50 000 | 1489776 | 53:12 | 1 or 2 dominant states per trajectory | 27198820 | 23:32:15 | various loop configurations |
a
Atom counts are the number actually used in clustering—heavy atoms for nucleic acids and α carbons for proteins. On three systems (noted with **) HDBSCAN clustering completed too quickly for the distributed computing environment to record the amount of memory consumed. Visualization of structures from additional systems and brief analysis are given in Supporting Information, Figures S11–S20.