Appendix 1 E-Predict Algorithm

Require: t, R, b, nt, λ

1: ∏ = ∅

2: for each protein p ∈ R do

3:    if p·fold ∉ ∏ then

4:       ∏ = ∏ ∪ {p·fold}

5:       Count[p·fold] ← 1

6:    else

7:       Count[p·fold] ← Count[p·fold] + 1

8:    end if

9: end for

10: for i ← 0 to |∏| - 1 do

11:    if Count[i] <nt then

12:       ∏ ← ∏ - {i}

13:    end if

14:    $E_{sum}^t$[i] ← 0

15:    Count[i] ← 0

16: end for

17: for each candidate SCOP fold F∈ ∏ do

18:    for each p ∈ R starting from the top ranked protein do

19:       if p·fold = F then

20:          Count[F] ← Count[F] + 1

21:          if Count[F] <nt then

22:             $E_{sum}^t$ [F] ← $E_{sum}^t$ [F] + E_Measure(p, b)

23:          end if

24:       end if

25:    end for

26: end for

27: F* ← arg minf $E_{sum}^t$[f]

28: if (λ = on) AND (S(t,P0) < S(t,$P_{NN}^{F*}$)) then

29:    F* ← P0.fold

30: end if

31: return F*