Supporting information

Transcript

1 Supporting information This supplementary information file contains the following: Algorithm 1: Side chain filtering and total partial loop conformation energy Table S1: sampling comparison between the algorithm and on the LoopBuilder dataset. Includes the case where samples with the energy function. Table S2: Full data table of sampling results of and the algorithm on each target of the LoopBuilder set Figure S1: Plots of the ( energy, ) pairs of the lowest energy conformation sampled by the algorithm and for each loop target of the LoopBuilder set, by loop length. Algorithm 1: Side chain filtering and total partial loop conformation energy All energies E are evaluated on the energy function chosen by the user Let E bb denote the total energy of the backbone, i.e. the N, C α, C, O, and C β atoms For each partial loop of length l with backbone energy E bb : Sample a maximum of n rot rotamers for residue l 0 + 1, with probability of rotamer i selected exp( Ei rot ) without replacement For j = 1, 2,..., n rot Attach side chain rotamer j on residue l and let Ej rot denote its energy If l 0 = 0 Save rotamer j as a side chain rotamer combination for residue 1 If l 0 > 0 Endif Endfor For k = 1, 2,..., n sc Attach saved side chain rotamer combination k on residues 1 to l 0 and let Ek tot be its total energy Calculate the two interaction energies: Ek bbsc = energy of res l backbone with rotamer combination k on 1 to l 0 Ej,k scsc = energy of rotamer j on l with rotamer combination k on 1 to l 0 The total side chain energy of this combination is Endfor Ej,k tot = Erot j + Ek tot + Ek bbsc + Ej,k scsc Select lowest n sc energies to be saved side chain rotamer combinations for res 1 to l The total energy of the partial loop conformation is E bb + min(e tot j,k ) Endfor 1

2 Table S1. sampling comparison between the algorithm and on the LoopBuilder dataset. Columns 3-7 represent respectively: average minimum energy found by sampling with the energy function, average minimum energy found by sampling with the +BBT energy function, average minimum energy found by the algorithm, average energy of the native loop conformations, number of cases where the minimum energy found by is lower than that found by the algorithm. Length Targets 1 2 Native < (out of 63) (out of 56) (out of 40) (out of 54) (out of 40) (out of 40) 1 : sampled with energy 2 : sampled with +BBT energy 3 : using results from column 4 for the comparison 2

3 Table S2. and comparison between and the algorithm, on each target of the LoopBuilder set. "MinE" is the lowest energy conformation sampled, and " of MinE" is the to native of that conformation. The energy of the native loop conformation is also shown. For sampling, uses the +BBT energy function following the conclusion of Section 3.2. Loop Native Protein Residues MinE of MinE MinE of MinE 135l a3c a a ads alc amm amm arb arb arb aru btkA btkA btl c cex clc cvl cvl ddt ezm fnd gof hbq iab lit lst mpp mrp msi nar nfp nif nif nls nwpA oyc poa

4 1ppn prn rro sbp thw tml wer wer xnb arcA ayh ayh ayh cmd ctc exo sga nul seb p ptp ptp rsa dfr Length 8 averages aac aba amp arb arb arp aru btl byb cseE csh ede fus fus gpr isuA ivd lkkA lkkA mla

5 1mrj mrk mrp nfp nif nls noa noa noa npk onc pda pgs php ptf ra rhs sgpE tca tca wer xif xnb xnb xyzA xyzA ayh cpl eng hbg sil pte pte pte tgl gcr Length 9 averages l ads ads amp arb arp aru avmA

6 1btl dim dim ede edg ezm fkf gpr gvp ixh knt mrj onc pgs plc ppn scs tca tca whi alp ayh cmd mnr sil hsc seb tgl fgf rsa rsa rsa Length 10 averages l a2pA a2yA a8d ads ako akz aol aru awqA bolA bx4A

7 1c5eA cb0A cnv cs6A cvl dad dysA edt eur exmA f46A fus g6sA g9gA gmuA gqvA i4jA iu8A ixh jp4A k7iA lmiA mla my7A nlnA nls nogA nscA ojqA othA oyc pgs pkhA qlwA rcf t1dA whi eng pth tgi pte pti Length 11 averages l a8d

8 1akz aozA arb arb bhe bkf bn8A c5eA cb0A cb8A cex cnv cs6A dim dqzA el5A exmA f46A i7pA iooA ixh iyeA jp4A kcmA lucA m3sA ms9A my7A othA oyc pkhA qlwA t1dA xyzA ayh hlcA pia ptd Length 12 averages pk a8d a8d arb bhe bkpA

9 1cnv cruA dpgA dqzA dysA ed8A eokA f46A g8fA gpiA hnjA hxhA iirA jp4A kblA krhA l8aA lki m3sA mo9A nlnA o6lA ockA ojqA os8A p1mA qqp qslA xyzA yge hlcA olbA ptd grs Length 13 averages

10 Figure S1. Plots of the ( energy, ) pairs of the lowest energy conformation sampled by the algorithm and for each loop target of the LoopBuilder set, by loop length. Length 8 loops Length 9 loops Length 10 loops Length 11 loops Length 12 loops Length 13 loops