Peptiderive Job Example run; Eph receptor - ephrin complex (3gxu) 「№19805」 Details

Inputs

Status

[complex.pdb]

Job ID19805
Job NameExample run; Eph receptor - ephrin complex (3gxu)
VisibilityPUBLIC
ProtocolPeptiderive
CPU hours used0.4
user
StatusExample
Description

peptide_lengths10
restrict_partners_to_chains
restrict_receptors_to_chains

Submitted time2015-12-30 11:14
Start time2015-12-30 11:15
End time2015-12-30 13:46

DaemonTACC.Stampede-4


Output

Derived peptides

Each tab shows information for the peptide derived from a certain chain pair and of a certain length.

[Download AB_10aa_in_context]

The receptor-partner complex, with the derived peptide highlighted.

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[Download AB_10aa]

Close-up of the derived peptide (positions 82-91) and the receptor.

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Peptide score vs. window position (receptor = chain A, peptide = chain B)

Total interface score: -30.64 REU

The score for each derived peptide vs. position from which the peptide window starts. Lower scores represent lower energy complexes. Cyclization candidates are highlighted in red. Hover on points for more information.

Background colors indicate the peptide interface score fraction from the total interface score

less than 5%
between 5-35%
between 35-50%
more than 50%
[Download BA_10aa_in_context]

The receptor-partner complex, with the derived peptide highlighted.

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[Download BA_10aa]

Close-up of the derived peptide (positions 27-36) and the receptor.

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Peptide score vs. window position (receptor = chain B, peptide = chain A)

Total interface score: -30.64 REU

The score for each derived peptide vs. position from which the peptide window starts. Lower scores represent lower energy complexes. Cyclization candidates are highlighted in red. Hover on points for more information.

Background colors indicate the peptide interface score fraction from the total interface score

less than 5%
between 5-35%
between 35-50%
more than 50%

Raw report file

[Download report file]
# Peptiderive report file complex - Chains: 2 - Fold tree: FOLD_TREE EDGE 1 171 -1 EDGE 1 172 1 EDGE 172 309 -1 ## Best cyclizable peptides for all chain pairs | Receptor | Partner | Peptide length | Position | Interface score | Disulfide info | Cyclized interface score | Sequence | |----------|---------|----------------|----------|-----------------|------------------------------|--------------------------|----------------------| | B | A | 10 | 123 | -0.287 | A_122-133 | N/A | TQVDIGDRIM | ## Best linear peptides for all chain pairs | Receptor | Partner | Peptide length | Position | Interface score | Disulfide info | Cyclized interface score | Sequence | |----------|---------|----------------|----------|-----------------|------------------------------|--------------------------|----------------------| | A | B | 10 | 82 | -17.654 | | N/A | KFQEFSPNLW | | B | A | 10 | 27 | -12.859 | | N/A | EEVSIMDEKN | ## All peptides - Options: pep_lengths= 10 is_skip_zero_isc= 1 is_do_minimize= 1 ### Receptor= A Partner= B Peptide_length= 10 - Total interface score: -30.6395 | Position | Interface score | Disulfide info | Cyclized interface score | |----------|-----------------|------------------------------|--------------------------| | 1 | -0.054 | | N/A | | 2 | -0.294 | | N/A | | 3 | -0.043 | | N/A | | 24 | 0.252 | | N/A | | 25 | 0.252 | | N/A | | 26 | 0.252 | | N/A | | 27 | 0.252 | | N/A | | 28 | 0.252 | | N/A | | 29 | 0.252 | | N/A | | 30 | 0.030 | | N/A | | 31 | 0.000 | | N/A | | 32 | 0.251 | | N/A | | 33 | 0.251 | | N/A | | 64 | -0.501 | | N/A | | 65 | -0.500 | | N/A | | 66 | -0.517 | | N/A | | 67 | -0.225 | | N/A | | 68 | -0.230 | | N/A | | 69 | -0.795 | | N/A | | 70 | -2.542 | | N/A | | 71 | -6.650 | | N/A | | 72 | -7.078 | | N/A | | 73 | -10.032 | | N/A | | 74 | -10.042 | | N/A | | 75 | -10.977 | | N/A | | 76 | -10.632 | | N/A | | 77 | -12.636 | | N/A | | 78 | -13.993 | | N/A | | 79 | -15.291 | | N/A | | 80 | -13.529 | | N/A | | 81 | -11.946 | | N/A | | 82 | -17.654 | | N/A | | 83 | -16.228 | | N/A | | 84 | -16.314 | | N/A | | 85 | -17.044 | | N/A | | 86 | -16.924 | | N/A | | 87 | -13.932 | | N/A | | 88 | -11.640 | | N/A | | 89 | -8.463 | | N/A | | 90 | -6.739 | | N/A | | 91 | -6.574 | | N/A | | 92 | -0.833 | | N/A | | 93 | -1.202 | | N/A | | 94 | -1.244 | | N/A | --- - Options: pep_lengths= 10 is_skip_zero_isc= 1 is_do_minimize= 1 ### Receptor= B Partner= A Peptide_length= 10 - Total interface score: -30.6395 | Position | Interface score | Disulfide info | Cyclized interface score | |----------|-----------------|------------------------------|--------------------------| | 1 | 0.000 | | N/A | | 2 | 0.000 | | N/A | | 3 | -0.281 | | N/A | | 4 | -0.445 | | N/A | | 5 | -0.785 | | N/A | | 6 | -0.800 | | N/A | | 7 | -0.800 | | N/A | | 8 | -0.800 | | N/A | | 9 | -0.800 | | N/A | | 10 | -0.786 | | N/A | | 11 | -0.769 | | N/A | | 12 | -0.741 | | N/A | | 13 | -0.296 | | N/A | | 14 | -0.102 | | N/A | | 15 | 0.000 | | N/A | | 16 | 0.000 | | N/A | | 17 | 0.000 | | N/A | | 18 | -1.883 | | N/A | | 19 | -1.783 | | N/A | | 20 | -3.643 | | N/A | | 21 | -7.366 | | N/A | | 22 | -9.745 | | N/A | | 23 | -10.627 | | N/A | | 24 | -11.353 | | N/A | | 25 | -12.787 | | N/A | | 26 | -12.748 | | N/A | | 27 | -12.859 | | N/A | | 28 | -10.674 | | N/A | | 29 | -10.706 | | N/A | | 30 | -7.666 | | N/A | | 31 | -5.526 | | N/A | | 32 | -2.651 | | N/A | | 33 | -2.286 | | N/A | | 34 | -2.759 | | N/A | | 35 | -2.561 | | N/A | | 36 | -2.945 | | N/A | | 37 | -2.744 | | N/A | | 38 | -2.746 | | N/A | | 39 | -2.463 | | N/A | | 40 | -2.441 | | N/A | | 41 | -1.964 | | N/A | | 42 | -1.930 | | N/A | | 43 | -1.836 | | N/A | | 44 | -0.092 | | N/A | | 45 | 0.000 | | N/A | | 66 | -0.049 | | N/A | | 67 | -0.305 | | N/A | | 68 | -0.358 | | N/A | | 69 | -3.680 | | N/A | | 70 | -3.732 | | N/A | | 71 | -3.784 | | N/A | | 72 | -3.836 | | N/A | | 73 | -3.810 | | N/A | | 74 | -4.945 | | N/A | | 75 | -5.659 | | N/A | | 76 | -5.611 | | N/A | | 77 | -5.124 | | N/A | | 78 | -4.831 | | N/A | | 79 | -1.719 | | N/A | | 80 | -1.719 | | N/A | | 81 | -1.719 | | N/A | | 82 | -1.719 | | N/A | | 83 | -1.486 | | N/A | | 84 | -0.492 | | N/A | | 115 | -1.616 | | N/A | | 116 | -0.174 | | N/A | | 117 | -1.020 | | N/A | | 118 | -1.064 | | N/A | | 119 | -1.068 | | N/A | | 120 | -1.065 | | N/A | | 121 | -1.048 | | N/A | | 122 | -1.901 | | N/A | | 123 | -0.287 | A_122-133 | N/A | | 124 | -0.290 | | N/A | | 125 | -0.939 | | N/A | | 126 | -1.477 | | N/A | | 127 | -1.563 | | N/A | | 128 | -1.583 | | N/A | | 129 | -1.583 | | N/A | | 130 | -1.583 | | N/A | | 131 | -1.536 | | N/A | | 132 | -0.738 | | N/A | | 133 | -0.726 | | N/A | | 134 | -0.697 | | N/A | | 155 | -2.432 | | N/A | | 156 | -2.394 | | N/A | | 157 | -2.394 | | N/A | | 158 | -2.394 | | N/A | | 159 | -2.382 | | N/A | | 160 | -1.353 | | N/A | | 161 | -0.887 | | N/A | | 162 | -0.293 | | N/A | --- *end of report*
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Scores




[Download all job files as tar archive]

[Input files (FS view)]
[Full set of decoy structures created on this run (FS view)]

[Input json]
[Output json]


Please cite the following article when referring to results from our ROSIE server:

  1. Yuval Sedan, Orly Marcu,Sergey Lyskov, Ora Schueler-Furman Peptiderive server: derive peptide inhibitors from protein–protein interactions Nucleic Acids Research 2016; doi: 10.1093/nar/gkw385 online

  2. London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O. (2010). Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins, 78:3140-49. [PMID: 20607702]

  3. Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R., "Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)". PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. Link


The ROSIE Peptiderive app was developed by Yuval Sedan at the Furman Lab, HUJI.