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EvoDesign Results for Monomer Example

[Click on PD133.tar to download the tarball file including the EvoDesign results listed on this page]


  Summary of Input
Scaffold Structure


  Top 10 Structural Homologs Used for Profile Construction

Rank PDB
Hit
TM-scoreIden.                    20                  40                  60      
                   |                   |                   |       
Sec.Str
Seq
CCCHHCECCEEEEEEEECCCCEEEEEEECCCCEEEEEECHHHHHHCCCCCCCEEEEEEEHCEEEEEC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
11gugA0.940.96 -SIARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
21h9jA0.920.39 MKIARNVFKGTVSALKEGAVNAEVDILLGGGDKLAAVVTLESARSLQLAAGKEVVAVVKAPWVLLMT
31fr3L0.90.33 MKIGRNKLEATVKEIVKGTVMAKIVMDYK-GTELVAAITIDSVADLDLVPGDKVTALVKATEMEVLK
41b9nA0.890.21 AQNADNQLPGIISHIERGAEQCEVLMALPDGQTLCATVPVNEAT--SLQQGQNVTAYFNADSVIIAT
53d31A0.850.24 STQIRNSLQGRVTEAWVLGALVRVKVDCG--VPLNVLITRRSAEEMELSPGVQIYARFKASSVHVLR
62awnB0.790.16 SDIADVILEGEVQVVEQLGNETQIHIQIPSIRNLVYRQNDV-V---LVEEGATFAIGLPPERCHLFR
73gd7A0.780.15 SDAD-VILEGEVQVVEQLGNETQIHIQIPSIRNLVYRQNV--VL---VEEGATFAIGLPPERCHLFR
82d62A0.760.19 -HDVENTVKATVDIIENLGGEKIVHLRR-GNISFTAKFPKE-S---KVREGDEVSVVFD-KKIHIFR
94tquS0.750.18 EGSERAQIKATVDIVEPLGSESILHATV-GDHSLVVKVGG--LN--EVHPGDPVTLHVDLTRVHLFD
101vciA0.750.09 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
Download evolutionary profile

  Clustering Results

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
147.27%5 Clus 1 Sequences
234.82%3 Clus 2 Sequences
39.10%1 Clus 3 Sequences
46.76%1 Clus 4 Sequences

  Summary of Output

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.

  Final Designed Sequences

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.
  Cluster 1 Center

Design
Number
EnergyIden. (%)
1-88.63 25.4 DSSP_SS
Scaffold

Design1
CCCHHHEECEEEEEEEECCCCEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCEEEEEEECCEEEEEC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
   | |  || |     |    ||   | ||   |        | |    | | |            
QKAAKNMYKGTVKEIEQGGSETEVYVQIPGGEELTMTMPIQTAEALKLEPGREITVIMPPDSIHVFR

  Cluster 1 Lowest Energy Sequences

Design
Number
EnergyIden. (%)
2-87 28.4 DSSP_SS
Scaffold

Design2
CCCHHHEECEEEEEEEECCCCEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCEEEEEEECCEEEEEC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
|  | | |||  |  |      |   || ||  |       | |      ||            |  
SKAAENTLKGRIVQVKELGQFTEIIVEIPGGEEIVMLVPVKSAEAMRLEPGAHIAVWIEASKIHIFK
3-84.03 17.9 DSSP_SS
Scaffold

Design3
CCCHHHEECEEEEEEEECCCCEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCEEEEEEECCEEEEEC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
     |   |  |            | | ||           |       ||      |     |  
RKPVENVYEGRIVHIEELGEETQIHLQIPGGQSLMAKVPVECVQTMKLEPGANVVVLMKADRIHIFR
4-85.38204 25.4 DSSP_SS
Scaffold

Design4
CCCHHHEECEEEEEEEECCCCEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCEEEEEEECCEEEEEC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
   | |   | |     |    |   |  ||           |||  |  |   |       | |  
EKVADNVFEGRVSFIERGGDYCEIHIECGGGENLKILVPVEAVEEMKVEPGKHITVLIPASNVHIFR
5-82.10587 26.9 DSSP_SS
Scaffold

Design5
CCCHHHEECEEEEEEEECCCCEEEEEEECCCCEEEEEEEHHHHHHCCCCCCCEEEEEEECCEEEEEC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
   | |  || ||    |    ||     ||   |  |            ||  |   |      | 
CKAADNIFKGRVVEIEMGGDYTEVIVKMPGGQSLTAVIPMKKANQMKIEQGAQVTVYMKADIIHVLR

  Cluster 2 Center

Design
Number
EnergyIden. (%)
6-84.03 35.8 DSSP_SS
Scaffold

Design6
CCCHHHHHCCEEEEEEECCHHEEEEEECCCCCCEEEEEEHHCCCCCCCCCCCEEEEEEECHEEEECC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
|  | | |||||    |     |    | || ||   |       || | | |   |     | |  
SSTAENILKGKVIKVEKLGELTEIYIAIPGGEKIAVLIPIECASDLGLKPGDEIVVVFPASSVHIFH

  Cluster 2 Lowest Energy Sequences

Design
Number
EnergyIden. (%)
7-85.38 29.9 DSSP_SS
Scaffold

Design7
CCCHHHHHCCEEEEEEECCHHEEEEEECCCCCCEEEEEEHHCCCCCCCCCCCEEEEEEECHEEEECC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
|    |  || |  |       |||    ||           || |    |    |  | | | |  
SRAVENLFKGRVDFLESLGDKTEVVMVVPGGQQLVVVVPIQCVEALKISPGQQIVAWFKPTQVHIYR
8-79.36452 31.3 DSSP_SS
Scaffold

Design8
CCCHHHHHCCEEEEEEECCHHEEEEEECCCCCCEEEEEEHHCCCCCCCCCCCEEEEEEECHEEEECC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
|      | | ||    |    | |  | || ||       | | | | |||          |    
SKALEYVLEGTVVAVEMGGEFTEIVMQIPGGKKIVVKVPVNSAEALQVTEGASVLVWMPPESVHVIR

  Cluster 3 Center

Design
Number
EnergyIden. (%)
9-82.11 26.9 DSSP_SS
Scaffold

Design9
CCCHHHEHECEEEEEEHCCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEEECCCHEEECC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
|      |||  | |  |     |     || | |  |      ||    |           |  | 
SKVTDYVLKGTIVQLELGGTETQVHIAVDGGQKLTVLIPIEQAQELKLQPGRKIIVWLPADQVHVLR


  Cluster 4 Center

Design
Number
EnergyIden. (%)
10-81.45 32.8 DSSP_SS
Scaffold

Design10
CCCHHHHHEEHHHHHHHCCCCEEEEEECCCCHEEEEEECHCHHHHHCCCCCCEEEEEECCCHEEECC
SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
  |  |   | |  |    | |||   | ||   |    | ||| |    |      |    | |  
QKSVDNLYEGTVTALQMMGVMAEVYIKIPGGQVLTALVPLNSVEQLKLQPGKHIIIYVPASKVHIMR


  I-TASSER Modeling of Designed Sequences


Models of Top 10 Designed Sequences

Click
to view
Design
#
TM-scoreRMSDC-scoreModel
Structure
1 0.911.02 0.56 Download
2 0.930.85 -0.14 Download
3 0.873.86 0.10 Download
4 0.901.04 -0.21 Download
5 0.901.15 -0.02 Download
6 0.891.20 0.08 Download
7 0.901.12 -0.19 Download
8 0.930.81 0.01 Download
9 0.881.47 0.10 Download
10 0.921.06 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.



Reference: