Molecular dynamics data
for protein complexes.

DynoDB integrates molecular dynamics (MD) trajectories and analysis results generated from a comprehensive data processing and simulation pipeline to support simulation studies on protein-protein complex interaction interfaces.

Search
ExampleshivhumanFabH1a2y

Dataset Statistics

PDB systems (6,282)

01,0002,0003,0004,000CountVH domain-Antigen: 2,783 (44.3%)2,783(44.3%)VH domain-AntigenLoop-mediated Dimer: 2,776 (44.2%)2,776(44.2%)Loop-mediated Dim…VHH-Antigen: 723 (11.5%)723(11.5%)VHH-AntigenPDB system

Deposited year (6,282)

0200400600Count of entries1976: 11981: 11982: 51984: 11985: 11986: 21987: 11988: 41989: 21990: 21991: 101992: 161993: 101994: 231995: 271996: 351997: 521998: 491999: 682000: 482001: 582002: 482003: 902004: 1482005: 1962006: 2482007: 2602008: 1792009: 2272010: 2332011: 2982012: 2372013: 3472014: 2292015: 3662016: 1442017: 1662018: 2042019: 2592020: 4102021: 4992022: 6412023: 4102024: 262025: 119761989200220152025Deposit year

Experimental method (6,282)

02,0004,0006,0008,000CountX-RAY DIFFRACTION: 5,360 (85.3%)5,360(85.3%)X-rayELECTRON MICROSCOPY: 922 (14.7%)922(14.7%)EMMethod

Resolution (Å) (6,282)

00.20.40.6Density0.84-0.93: 20.93-1: 81-1.10: 241.10-1.19: 201.19-1.27: 391.27-1.36: 851.36-1.45: 701.45-1.53: 1561.53-1.62: 1741.62-1.71: 2471.71-1.80: 1651.80-1.88: 4171.88-2: 3992-2.06: 3672.06-2.14: 2662.14-2.23: 2892.23-2.32: 3062.32-2.40: 2542.40-2.49: 1222.49-2.58: 3422.58-2.66: 2782.66-2.75: 2912.75-2.84: 2852.84-2.92: 2642.92-3: 2833-3.10: 873.10-3.18: 2543.18-3.27: 2643.27-3.36: 2013.36-3.44: 1733.44-3.53: 1443.53-3.62: 13.62-3.71: 23.71-3.79: 03.79-3.88: 23.88-4: 04-4.05: 04.05-4.14: 04.14-4.23: 04.23-4.31: 11234Resolution (Å)

Single chain length (12,564)

00.0040.0080.0120.016Density7-21.8: 321.8-36.5: 2236.5-51.2: 2651.2-66: 26666-80.8: 19680.8-95.5: 42195.5-110: 1,368110-125: 3,490125-140: 1,214140-154: 647154-169: 845169-184: 654184-199: 726199-214: 634214-228: 359228-243: 302243-258: 303258-272: 179272-287: 143287-302: 108302-317: 174317-332: 172332-346: 87346-361: 52361-376: 46376-390: 27390-405: 31405-420: 9420-435: 21435-450: 11450-464: 7464-479: 4479-494: 5494-508: 3508-523: 2523-538: 2538-553: 2553-568: 1568-582: 0582-597: 20200400600Residues

Complex length (6,282)

00.0010.0020.0030.0040.005Density112-136: 19136-160: 25160-184: 137184-208: 695208-232: 660232-256: 698256-280: 755280-304: 703304-328: 853328-352: 357352-376: 170376-400: 139400-424: 143424-448: 111448-472: 108472-496: 130496-520: 108520-544: 75544-568: 47568-592: 51592-616: 35616-640: 85640-664: 44664-688: 35688-712: 23712-736: 12736-760: 15760-784: 8784-808: 15808-832: 4832-856: 5856-880: 8880-904: 2904-928: 2928-952: 0952-976: 2976-1000: 01000-1024: 11024-1048: 11048-1072: 1300600900Residues

Atom count (6,282)

01e-42e-43e-4Density899-1145: 231145-1392: 371392-1638: 4371638-1884: 1321884-2130: 1962130-2377: 2052377-2623: 2442623-2869: 3082869-3115: 3263115-3362: 5133362-3608: 5363608-3854: 5473854-4101: 4664101-4347: 5524347-4593: 3934593-4839: 5664839-5086: 4115086-5332: 1875332-5578: 1045578-5824: 335824-6071: 66071-6317: 206317-6563: 106563-6810: 46810-7056: 37056-7302: 47302-7548: 37548-7795: 37795-8041: 48041-8287: 18287-8534: 28534-8780: 08780-9026: 19026-9272: 09272-9519: 29519-9765: 19765-10011: 010011-10257: 010257-10504: 110504-10750: 1300060009000Atoms

Antibody type (3,506)

01,0002,0003,000CountFabH: 1,899 (54.2%)1,899(54.2%)FabHVH: 744 (21.2%)744(21.2%)VHVHH: 721 (20.6%)721(20.6%)VHHscFv: 122 (3.5%)122(3.5%)scFvVH+: 9 (0.3%)9(0.3%)VH+Others: 11 (0.3%)11(0.3%)OthersAntibody type

Antigen category (3,506)

05001,0001,5002,000CountVirus: 1,537 (43.8%)1,537(43.8%)VirusAnimalia: 1,311 (37.4%)1,311(37.4%)AnimaliaBacteria: 393 (11.2%)393(11.2%)BacteriaProtista: 125 (3.6%)125(3.6%)ProtistaPlantae: 49 (1.4%)49(1.4%)PlantaeOthers: 91 (2.6%)91(2.6%)OthersCategory

Antibody species (3,506)

01,0002,000CountHomo sapiens: 1,686 (48.1%)1,686(48.1%)Homo sapiensMus musculus: 872 (24.9%)872(24.9%)Mus musculusLama glama: 389 (11.1%)389(11.1%)Lama glamaVicugna pacos: 208 (5.9%)208(5.9%)Vicugna pacossynthetic construct: 100 (2.9%)100(2.9%)synthetic constru…Others: 251 (7.2%)251(7.2%)OthersSpecies

Antigen species (3,506)

05001,0001,500CountHomo sapiens: 1,041 (29.7%)1,041(29.7%)Homo sapiensSARS-CoV-2: 714 (20.4%)714(20.4%)SARS-CoV-2HIV-1: 208 (5.9%)208(5.9%)HIV-1Gallus gallus: 85 (2.4%)85(2.4%)Gallus gallusMus musculus: 71 (2.0%)71(2.0%)Mus musculusOthers: 1,387 (39.6%)1,387(39.6%)OthersSpecies

Binder species (2,776)

02505007501,000CountHomo sapiens: 764 (27.5%)764(27.5%)Homo sapiensHIV-1: 295 (10.6%)295(10.6%)HIV-1Escherichia coli: 98 (3.5%)98(3.5%)Escherichia coliMus musculus: 74 (2.7%)74(2.7%)Mus musculusBos taurus: 61 (2.2%)61(2.2%)Bos taurusOthers: 1,484 (53.5%)1,484(53.5%)OthersSpecies

Target species (2,776)

02505007501,000CountHomo sapiens: 770 (27.7%)770(27.7%)Homo sapiensHIV-1: 295 (10.6%)295(10.6%)HIV-1Escherichia coli: 103 (3.7%)103(3.7%)Escherichia coliMus musculus: 77 (2.8%)77(2.8%)Mus musculusBos taurus: 43 (1.5%)43(1.5%)Bos taurusOthers: 1,488 (53.6%)1,488(53.6%)OthersSpecies
Visits
2,984
Users
71
Activity · Last 30 Days
1,177
total visits
latest · 2026-10-31 · 20 visits
live stream
2026-10-022026-10-31

Referenced Databases

SAbDab logoRCSB PDB logoUniProt logo