Release Notes

v2.4.1 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

Changes in the default parameters¶

There are a lot of parameters that can be changed in the water bridge analysis, including the distances, angles, and the number of involved water molecules or residues.

atoms: Atomic object from which atoms are considered

method: 'cluster' or 'chain', where ‘chain’ will find the shortest: water bridging path between two protein atoms default is 'chain'
distDA: maximal distance between water/protein donor and acceptor: default is 3.5
distWR: maximal distance between considered water and any residue: default is 4
anglePDWA: angle range where protein is donor and water is acceptor: default is (100, 200)
anglePAWD: angle range where protein is acceptor and water is donor: default is (100, 140)
angleWW: angle between water donor/acceptor: default is (140, 180)
maxDepth: maximum number of waters in chain/depth of residues in cluster: default is 2
maxNumRes: maximum number of water+protein residues in cluster: default is None
donors: which atoms to count as donors: default is ['N', 'O', 'S', 'F']
acceptors: which atoms to count as acceptors: default is ['N', 'O', 'S', 'F']
output: return information arrays, (protein atoms, water atoms),: or just atom indices per bridge Options are 'info', 'atomic' and 'indices' Default is 'atomic'
isInfoLog: whether to log information: default is True

Here’s an example of how to apply changes in parameters:

In [1]: waterBridges_2 = calcWaterBridges(atoms, method='cluster', distWR=3.0, distDA=3.2, maxDepth=3)

@> 17 water bridges detected.
@> SER7 OG_21 A LYS110 NZ_838 A 4.70722699686344 1 ['A_1316']
@> GLY14 O_72 A SER47 O_328 A GLU50 N_347 A 5.288116583434976 4.544135231262378 5.10489901956934 1 ['A_1274']
@> PRO20 O_115 A GLU23 OE1_139 A 4.571172934816621 1 ['A_1292']
@> GLU23 OE2_140 A SER71 O_514 A HIS72 ND1_523 A 4.934310286149422 4.127239392136104 4.463734423103597 1 ['A_1244']
@> ASP42 OD2_301 A ARG40 NH2_286 A 5.163938516287738 1 ['A_1246']
@> ASP81 OD1_598 A THR84 OG1_621 A ARG40 NH2_286 A 4.415462942886057 4.365525627000715 3.9229717052255175 1 ['A_1262']
@> GLY14 O_72 A SER47 O_328 A GLU50 N_347 A 5.288116583434976 4.544135231262378 5.10489901956934 1 ['A_1274']
@> GLU50 OE2_355 A TYR131 OH_1009 A 5.157987010452818 1 ['A_1299']
@> ARG65 NH2_473 A ASP135 O_1037 A 4.820906553751068 1 ['A_1267']
@> GLU23 OE2_140 A SER71 O_514 A HIS72 ND1_523 A 4.934310286149422 4.127239392136104 4.463734423103597 1 ['A_1244']
@> GLN105 NE2_800 A LYS102 O_772 A LYS79 NZ_582 A 4.2363221076778395 3.8752885053889865 4.929221236666094 1 ['A_1249']
@> ASP81 OD1_598 A THR84 OG1_621 A ARG40 NH2_286 A 4.415462942886057 4.365525627000715 3.9229717052255175 1 ['A_1262']
@> GLN105 NE2_800 A LYS102 O_772 A LYS79 NZ_582 A 4.2363221076778395 3.8752885053889865 4.929221236666094 1 ['A_1249']
@> SER7 OG_21 A LYS110 NZ_838 A 4.70722699686344 1 ['A_1316']
@> LEU125 O_953 A GLY117 N_886 A 3.8595291163560352 1 ['A_1264']
@> GLU50 OE2_355 A TYR131 OH_1009 A 5.157987010452818 1 ['A_1299']
@> ARG65 NH2_473 A ASP135 O_1037 A 4.820906553751068 1 ['A_1267']