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Result of EvoDesign for MopII molbindin from Clostridium pasteurianum
Summary of input:
Summary of output:
- EvoDesign Rank: Top designed sequences ranked by decreasing order of cluster size. We suggest that you use Rank 1, which is lowest energy design after clustering.
- EvoDesign score: The confidence score of EvoDesign; the lower the score, the higher the confidence.
- Sequence Identity: The percentage of sequence identity between the design sequence and the scaffold sequence.
- Normalized Relative Error (NRE): NRE=(EDSāETS)/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 scaffold structure is assigned by DSSP program.
- Secondary Structure (SS): SS is predicted by PSSPred for scaffold and design sequences. The Q3 error on design sequence (EDS) and scaffold sequence (ETS) with respect to scaffold structure is used to calculate NRE on SS.
- 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.
- Torsion Angle (TA): TA is predicted by ANGLOR for scaffold and design sequences. The mean absolute difference of design sequence (EDS) and scaffold sequence (ETS) from scaffold structure is used for calculating NRE on TA.
- I-TASSER prediction: The design sequences are modeled by I-TASSER server. The structure of the first model of the I-TASSER prediction is made available at the Model column. The TM-score and RMSD of the I-TASSER predicted model with the scaffold structure is reported in the last two columns.
Details on Design: SeqIdentity: % of sequence identity between design sequence and scaffold sequence.
Lig_bind: Residues are within 8.0 Å sphere radius of the hetero atoms.
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.
Design 1:
Download Model
SeqIdentity: 25.4%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | || | | || | || | | | | | |
Design 1: QKAAKNMYKGTVKEIEQGGSETEVYVQIPGGEELTMTMPIQTAEALKLEPGREITVIMPPDSIHVFR
Design 2:
Download Model
SeqIdentity: 28.4%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | | ||| | | | || || | | | || |
Design 2: SKAAENTLKGRIVQVKELGQFTEIIVEIPGGEEIVMLVPVKSAEAMRLEPGAHIAVWIEASKIHIFK
Design 3:
Download Model
SeqIdentity: 17.9%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | | | | || | || | |
Design 3: RKPVENVYEGRIVHIEELGEETQIHLQIPGGQSLMAKVPVECVQTMKLEPGANVVVLMKADRIHIFR
Design 4:
Download Model
SeqIdentity: 25.4%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | | | | | | || ||| | | | | |
Design 4: EKVADNVFEGRVSFIERGGDYCEIHIECGGGENLKILVPVEAVEEMKVEPGKHITVLIPASNVHIFR
Design 5:
Download Model
SeqIdentity: 26.9%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | || || | || || | | || | | |
Design 5: CKAADNIFKGRVVEIEMGGDYTEVIVKMPGGQSLTAVIPMKKANQMKIEQGAQVTVYMKADIIHVLR
Design 6:
Download Model
SeqIdentity: 35.8%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | | ||||| | | | || || | || | | | | | |
Design 6: SSTAENILKGKVIKVEKLGELTEIYIAIPGGEKIAVLIPIECASDLGLKPGDEIVVVFPASSVHIFH
Design 7:
Download Model
SeqIdentity: 29.9%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | || | | ||| || || | | | | | | |
Design 7: SRAVENLFKGRVDFLESLGDKTEVVMVVPGGQQLVVVVPIQCVEALKISPGQQIVAWFKPTQVHIYR
Design 8:
Download Model
SeqIdentity: 31.3%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | | || | | | | || || | | | | ||| |
Design 8: SKALEYVLEGTVVAVEMGGEFTEIVMQIPGGKKIVVKVPVNSAEALQVTEGASVLVWMPPESVHVIR
Design 9:
Download Model
SeqIdentity: 26.9%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| ||| | | | | || | | | || | | |
Design 9: SKVTDYVLKGTIVQLELGGTETQVHIAVDGGQKLTVLIPIEQAQELKLQPGRKIIVWLPADQVHVLR
Design 10:
Download Model
SeqIdentity: 32.8%
Lig_bind: ** **
DSSP_SS: CCCCCCEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCC
Scaffold: SISARNQLKGKVVGLKKGVVTAEVVLEIAGGNKITSIISLDSVEELGVKEGAELTAVVKSTDVMILA
| | | | | | ||| | || | | ||| | | | | |
Design10: QKSVDNLYEGTVTALQMMGVMAEVYIKIPGGQVLTALVPLNSVEQLKLQPGKHIIIYVPASKVHIMR
Reference:
-
Robin Pearce, Dani Setiawan, Xiaoqiang Huang, Yang Zhang.
EvoDesign: Designing protein-protein binding interactions using evolutionary interface profiles,
in preparation.
- Pralay Mitra, David Shultis and Yang Zhang. EvoDesign: de novo protein design based on structural and evolutionary profiles.
Nucleic Acids Res. 41: W273-W280, 2013
(Download the PDF file)