Table 1 A summary of different restrain methods employed in the steered molecular dynamics simulation during the last three decades.
Nr | Year | Complex | Fixed atoms | PDB ID |
|---|---|---|---|---|
1 | 1997 | Bacteriorhodopsin and retinal (C20H28O) | Six atoms, the Cα—atoms of six residues, at the ends of helices A, B, and C16 | 1BRD |
2 | 1999 | Human retinoic acid receptor hRAR and retinoic acid (C20H28O2) | Set of atoms, all of Cα—atoms in the top part of the protein31 | 2LBD |
3 | 1999 | Gelsolin sesgment 1 and Adenosine-5'-triphosphate (C10H16N5O13P3) | Set of atoms, all carbon atoms of residues 31, 26, 56, 215, 307, and 333 at the front face of the protein33 | 1EQY |
4 | 2002 | Acetylcholine receptors and huperzine A (C15H18N2O) | Center of mass of AChE protein37 | 1VOT |
5 | 2003 | HIV-1 reverse transcriptase and (2-acetyl-5-methylanilino)(2,6-dibromophenyl)acetamide (C17H16Br2N2O2) | All heavy atom38 | 1HNI |
6 | 2005 | Acetylcholine receptors and 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine (C24H29NO3) | None report39 | 1EVE |
7 | 2006 | Acetylcholine receptors and acetylcholine (C7H16NO2+) | One atom, a Cα of residue V-10940 | 1I9B |
8 | 2010 | Neuraminidase and oseltamivir carboxylate (C14H24N2O4) | Center of mass of protein Cα—atoms32 | 2HU4, 3CL0, 3CL2 |
9 | 2015 | Thrombin and C32H35BrN2O2S, neuraminidase and C11H19NO9, penicillopepsin and alpha-D-mannopyranose (C6H12O6) | Set of atoms, Cα—atoms of the receptor which are 3 Å behind the last atom of the ligand41 | 1D3D, 1NSC, 1APT |
10 | 2015 | Bovine beta-lactoglobulin and octanoic acid (C8H16O2) | Cα—atoms far from binding site are fixed42 | 3NQ9 |
11 | 2019 | Human Adenosine A2A Receptor and C23H29N7O6, C16H15N7O2 | Five atoms, Cα—atoms of five residues at the top of the transmembrane helices (residues 9, 80, 177, 256 and 270)43 | 4UHR, 5IU4 |
12 | 2020 | Trypsin and benzamidine (C7H8N2) | All Cα—atoms44 | 3PTB |
13 | 2020 | Human Abl kinase domain and imatinib (C29H31N7O) | All backbone atoms of protein’s binding pocket45 | 2HYY |
14 | 2020 | RDB of Spike protein and simeprevir (C38H47N5O7S2), or lumacaftor (C24H18F2N2O5) | All atoms of protein backbone46 | 6LZG |
15 | 2021 | Heat shock protein 90 (Hsp90) and C13H10BrN5 | All Cα—atoms47 | 3K99 |
16 | 2022 | Spike protein of SAR-2 virus and ACE2 and silodosin (C25H32F3N3O4) | Cα—atoms of residues 519, 333, 360, 525, 386 and 517.48 | 6LZG |
17 | 2022 | Neuraminidase and capsaicin (C18H27NO3) | All Cα—atoms49 | 2HU0 |
