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Table 4 Counts of sequences and membrane helices of the data subsets used for the specialised benchmarks for channels reported in this paper

From: A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions

Channel structure family

Abbreviated channel structure family

#seqs

#TMH

#½MH

Total #MH

Channels: Formate Nitrate Transporter (FNT) Family

(1) FNT

3

19

3

22

Channels: Amt/Rh proteins

(2) Amt/Rh

6

67

0

67

Channels: Aquaporins and Glyceroporins

(3) Aquaporin

12

72

24

96

Channels: Gap Junctions

(4) Jap junction

1

4

0

4

Channels: Potassium and Sodium Ion-Selective

(5) K+ channel

25

80

25

105

Channels: Urea Transporters

(6) Urea transport

1

10

2

12

Channels: Other Ion Channels

(7) Other

14

37

0

37

  1. The benchmark server's membrane protein structure family selections were used to restrict each benchmark to a membrane channel structure family. There was no restriction on similarity (the benchmark server's similarity level was set to 100%), and for all other options the server's default parameters were used. Legend : #seqs : number of sequences; #TMH : number of transmembrane helices that cross the membrane; #½MH : number of half-membrane helices; Total #MH : total number of membrane helices.