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. Author manuscript; available in PMC: 2017 Oct 20.
Published in final edited form as: J Chem Theory Comput. 2016 Nov 7;12(12):5946–5959. doi: 10.1021/acs.jctc.6b00712

Table 1.

List of representative structures used for testing. Unless stated otherwise, the cutoff and threshold distances listed here were used for all testing.

Structure PDB ID Size (atoms) |Charge| (e) Cutoff dist (Å) drn (Å) for OPCA Threshold dist (Å)
h1 h2 h3
10 bp B-DNA fragment 2BNA 632 18 21 21 n/a n/a 0.35
Immunoglobulin binding domain 1BDD 726 2 15 15 n/a n/a 0.25
Ubiquitin 1UBQ 1231 1 15 15 n/a n/a 0.25
Thioredoxin 2TRX 1654 5 15 15 n/a n/a 0.35
Nucleosome core particle 1KX5 25101 133 21 21 90 n/a 0.1
Microtubule sheet * 158016 360 15 15 48 n/a 0.25
Virus capsid 1A6C 475500 120 15 15 66 n/a 0.25
Chromatin fiber ** 1159998 8238 21 21 90 169 0.35
*

The microtubule sheet was constructed as described in Wang and Nogales.97

**

The chromatin fiber was constructed as described in Wong et. al.98.