Round 26

Registration is closed Participant list

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Announcement

Target T53 a protein-protein complex (homology/unbound).
Target T54 a protein-protein complex (homology/unbound).
Target T55 (scoring only) is a large set (>500) of point mutations made in a protein engineered to bind another; given the X-ray structure of one complex, the challenge is to predict the effect of each mutation on the interaction.
Target T56 (scoring only) is a large set (>500) of point mutations made in a protein engineered to bind another; given the X-ray structure of one complex, the challenge is to predict the effect of each mutation on the interaction.

Background information for T55-56:

The experimental method for measuring the effects on affinity was amodified version of the Fowler et al. (Nature Methods 7:741, 2010) work.Briefly, starting from the tightest HB36 and HB80 variants of theoriginal de novo design report (Fleishman et al., Science 332 :816,2011), the Baker lab generated gene libraries encoding each of the 20amino acid residues at each position on these two binders (for HB80, thismeans ~53 positions x 20 aa identities each for a total diversity of>1000 variants). Weak selection for binding (and protein expressionand display, below) using yeast cell-surface display was then applied toselect substitutions that make small favorable contributions to bindingversus others that are deleterious or ineffective. Next-generation DNAsequencing of the starting (naive) library and the evolved library thenprovided a comparison of the propensities of individual clones in theselected and unselected libraries of each point substitution (e.g., didthe abundance of an interfacial Ala->Val variant increase/decrease/stay constantin the yeast population that was selected for binding?). In addition, the effects of the substitutions on expression levels were tested by either passaging the library withoutselection, or by selecting for higher expressing clones; in both cases noeffects on clonal distributions were discerned compared to the startingnaïve library, e.g., core substitutions from Trp to Asp were welltolerated in terms of expression (but were deleterious to binding),indicating that expression of HB36 and HB80 variants in yeast is veryrobust. In a second step (not subject to CAPRI prediction), the Baker labhas combined multiple point substitutions that individually make smallimprovements to binding, This has generated variants of the designs thatbind two orders of magnitude more tightly than the starting ones insurface plasmon resonance (SPR) experiments, providing independentcontrols for the ability of the selection approach to map energeticcontributions to binding.

Format for T55-56 submissions :

Each group should use the group number assigned to them in this round.Please see the website for participant number here
The participant number should be used in the place of X below.
Please send three separate e-mails to sameer AT ebi.ac.uk.

• One should have subject line " CAPRI Group X : T55-56 Methodology" and contain the names of participants, their affiliation, and a short description of the method. It will be hidden from the assessors.
• The email with results for target 55 should have subject line " CAPRI Group X : T55 results"
• The email with results for target 56 should have subject line " CAPRI Group X : T56 results"

As illustrated below, the results should comprise 20 records per mutated position n of the protein sequence; 
in each, XnY defines the mutant (XnX for the wild type), k, the predicted effect on the interaction 
(0=unknown, 1=deleterious, 2=neutral, 3=beneficial; wild type has k=2 by definition) ; 
s is a score scaled to range from 1.0 for the mutants with the highest chance of binding to 0.0 for those with the 
lowest chance; the wild type should be in between.

T55:

P23A k s 
....
P23Y k s
...
...
A76A k s
...
A76Y k s

Extension of CAPRI Round 26 for targets 55 and 56

David Baker, Sarel Fleishman and Rocco Moretti (University of Washington) have suggested that we extend Round 26 by adding a second step of T55-T56 predictions. Their data on about half of the mutants (strictly confidential) will be made accessible to registered Round 26 participants, who may use them to optimize prediction schemes and make a new set of predictions. It should concern only the withheld data and be submitted in the same format as the first set.

The file for experimental data on HB36.4 mutants contains two columns "mutant definition" and "log2 values of enrichment ratios" for target T55(scoring only) in the following format

mut log2_ratio
P23P -0.454741086
P23E -1.958972314
etc.

The file for experimental data on HB80.3 mutants contains two columns "mutant definition" and "log2 values of enrichment ratios" for target T56(scoring only) in the following format

mut log2_ratio
P10P -0.387525485
P10C -3.156912561
etc.

Round 26 of CAPRI has four targets
Note to server managers: T53-T54 require some model building, and automatic 
servers will have 72 hours to make submissions.
T53 - a protein-protein complex (homology/unbound) 

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Targets

Dates

Registration starts: Nov. 2, 2011, midnight

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