Scaffold Structure

Rank	PDB Hit	TM-score	Iden.		20                  40                  60                          |                   |                   |
				Sec.Str Seq	CCCHHCECCEEEEEEEECCCCEEEEEEECCCCEEEEEECHHHHHHCCCCCCCEEEEEEEHCEEEEEC SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
1	1gugA	0.94	0.96		-SIARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
2	1h9jA	0.92	0.39		MKIARNVFKGTVSALKEGAVNAEVDILLGGGDKLAAVVTLESARSLQLAAGKEVVAVVKAPWVLLMT
3	1fr3L	0.9	0.33		MKIGRNKLEATVKEIVKGTVMAKIVMDYK-GTELVAAITIDSVADLDLVPGDKVTALVKATEMEVLK
4	1b9nA	0.89	0.21		AQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEAT--SLQQGQNVTAYFNADSVIIAT
5	3d31A	0.85	0.24		STQIRNSLQGRVTEAWVLGALVRVKVDCG--VPLNVLITRRSAEEMELSPGVQIYARFKASSVHVLR
6	2awnB	0.79	0.16		SDIADVILEGEVQVVEQLGNETQIHIQIPSIRNLVYRQNDV-V---LVEEGATFAIGLPPERCHLFR
7	3gd7A	0.78	0.15		SDAD-VILEGEVQVVEQLGNETQIHIQIPSIRNLVYRQNV--VL---VEEGATFAIGLPPERCHLFR
8	2d62A	0.76	0.19		-HDVENTVKATVDIIENLGGEKIVHLRR-GNISFTAKFPKE-S---KVREGDEVSVVFD-KKIHIFR
9	4tquS	0.75	0.18		EGSERAQIKATVDIVEPLGSESILHATV-GDHSLVVKVGG--LN--EVHPGDPVTLHVDLTRVHLFD
10	1vciA	0.75	0.09		E--RTARLIGKVDFVEALGTDTILHVKFG-DELVKVKLPGH-IP---IEPGREVKVIMDLDMIHVFD
(a) All the residues are colored in black; however, those residues in the homolog that are identical to the residues in the scaffold sequence are highlighted in color. The coloring scheme is based on the property of the amino acid, where polar residues are brightly colored and non-polar residues are colored in darker shades. (more about the colors used) (b) Homologs used for profile construction are ranked by TM-score. (c) TM-score is calculated between the scaffold structure and each identified homolog. The higher the TM-score, the more similar the structure. (d) Iden. is the percent sequence identity between the scaffold and each homolog.

Download full multiple sequence alignment
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Sequences generated during the Monte Carlo simulation are clustered. The top clusters are listed in the table below. Information in the table includes the relative cluster sizes as well as the number of the top sequences that originate from each cluster. Users are able to download every sequence in each cluster; the files include the sequences as well as the free-energy of each sequence predicted by EvoDesign.

Cluster Number	Relative Cluster Size	# Sequences Selected from Cluster	Download Each Sequence in Cluster
1	47.27%	5	Clus 1 Sequences
2	34.82%	3	Clus 2 Sequences
3	9.10%	1	Clus 3 Sequences
4	6.76%	1	Clus 4 Sequences

Design Number	Sequence Identity (%)[?]	Normalized Relative Error [?]
		Secondary Structure	Solvent Accessibility	Torsion Angle φ	Torsion Angle ψ
Design 1	25.4	-0.13	-0.07	0.07	0.30
Design 2	28.4	0.47	0.04	0.47	0.73
Design 3	17.9	0.07	0.07	0.05	0.04
Design 4	25.4	-0.13	-0.14	0.49	0.53
Design 5	26.9	-0.27	0.06	0.01	0.28
Design 6	35.8	0.53	0.06	0.24	0.14
Design 7	29.9	0.60	-0.08	0.53	1.51
Design 8	31.3	0.33	0.02	0.53	0.79
Design 9	26.9	-0.27	0.09	0.49	0.27
Design 10	32.8	0.47	0.09	0.25	0.93
Data.zip	SI	SS	SA	φ	ψ

(a)	Sequence Identity: The percent sequence identity between the designed sequence and the scaffold sequence.
(b)	Normalized Relative Error (NRE): NRE=(EDS−ETS)/ETS, where EDS is the error of the neural-network predictions relative to the scaffold structure on the design sequence and ETS is the error of the predictions based on the sequence of the target scaffold. The secondary structure, solvent accessibility and torsion angles for the scaffold structure are assigned by DSSP.
(c)	Secondary Structure (SS): SS is predicted by PSSPred for the scaffold and design sequences. The Q3 errors of the design sequence (EDS) and scaffold sequence (ETS) with respect to the scaffold structure are used to calculate the NRE for SS.
(d)	Solvent Accessibility (SA): SA for scaffold and design sequences are predicted by neural-network method. The correlation on SA between design sequence and scaffold structure (EDS) and between scaffold sequence and scaffold structure (ETS) is used to calculate NRE on SA.
(e)	Torsion Angle (TA): TA is predicted by ANGLOR for scaffold and design sequences. The mean absolute difference of the design sequence (EDS) and scaffold sequence (ETS) from the scaffold structure is used to calculate NRE for TA.

Energy:         EvoDesign calculated free energy of binding and folding
 Iden.:         % of sequence identity between design sequence and scaffold sequence.
DSSP_SS:        Secondary structure as assigned by DSSP program on the scaffold structure.
Scaffold:       Scaffold sequence.
                The identical residues are marked by '|'.
Design:         Design sequence.

Models of Top 10 Designed Sequences Click to view Design # TM-score RMSD C-score Model Structure 1 0.91 1.02 0.56 Download 2 0.93 0.85 -0.14 Download 3 0.87 3.86 0.10 Download 4 0.90 1.04 -0.21 Download 5 0.90 1.15 -0.02 Download 6 0.89 1.20 0.08 Download 7 0.90 1.12 -0.19 Download 8 0.93 0.81 0.01 Download 9 0.88 1.47 0.10 Download 10 0.92 1.06 0.11 Download (a) TM-score is calculated between the designed sequence and the scaffold structure. (b) RMSD is calculated between the designed sequence and the scaffold structure. (c) C-score typically ranges from [-5,2] and is a quantitative measure of the confidence of each model. The higher the C-score, the higher the confidence in the model.