Fold Recognition

Ole Lund,
Assistant professor,
CBS
Fold recognition

 Find template for modeling

– 1st step in comparative modeling
 Can be used to predict function

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Template identification

 Search with sequence

– Blast against proteins with known structure
– Psi-Blast against all proteins
– Fold recognition methods
 Use biological information
 Functional annotation in databases
 Active site/motifs

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Blast derivatives: PDB-BLAST

 Procedure
1. Build sequence profile by iterative PSI-BLAST
search against a sequence database
2. Use profile to search database of proteins with
known structure
 Advantage
– Makes sure hid to protein with known structure is
not hidden behind a lot of hits to other proteins

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BLAST derivatives: Transitive BLAST

 Procedure
1. Find homologues to query (your) sequence
2. Find homologues to these homologues
3. Etc.
– Can be implemented with e.g. BLAST or PSI-
BLAST
 Also known as Intermediate Sequence
Search (ISS)

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CASP

 CASP
– Critical Assessment of Structure Predictions
– Every second year
– Sequences from about-to-be-solved-structures
are given to groups who submit their predictions
before the structure is published
– Modelers make prediction
– Meeting in Asilomar where correct answers are
revealed

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Target difficulty

 CM: Comparative (homology) modeling

 CM/FR: not PSI-BLAST (but ISS) findable
 FR(H): Homologous fold recognition
 FR(A): Analogous fold recognition
 NF/FR: Partly New fold
 NF: New Fold (used to be called Ab Initio -
from first principles- prediction)

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CASP5
overview

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Successful fold recognition groups at
CASP5

 3D-Jury (Leszek Rychlewski)

 3D-CAM (Krzysztof Ginalski)
 Template recombination (Paul Bates)
 HMAP (Barry Honig)
 PROSPECT (Ying Xu)
 ATOME (Gilles Labesse)

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3D-Jury (Rychlewski)

 Inspired by Ab initio modeling methods

– Average of frequently obtained low energy structures is
often closer to the native structure than the lowest energy
structure
 Find most abundant high scoring models
1. Use output from a set of servers
2. Superimpose all pairs of structures
3. Similarity score Sij = # of Ca pairs within 3.5Å
(if #>40;else Sij=0)
4. 3D-Jury score = SiSij/(N+1)
 Similar methods developed by A Elofsson (Pcons)
and D Fischer (3D shotgun)

Rychlewski.doc OL
 Ginalski.doc

3D-CAM (Krzysztof Ginalski)

 3D-Consensus Alignment Method
– Structural alignment for all members of fold from FSSP
– Conservation of specific residues and contacts
 responsible for maintaining tertiary structure
 critical for substrate binding and/or catalysis
– Find homologues with iterative PSI-BLAST
– Align with ClustalW – identify conserved residues
– Structural integrity of alignments
– Manual realignment
– Fold recognition for homologues
– Modelling
– Verification
 Visually
 Computationally (Verify3D, ProsaII, WHAT_CHECK)
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 Abstract

Paul A Bates - In Silico Recombination

of Templates, Alignments and Models

 Problems
– Models rarely better than templates
– Manual intervention have marginal effect
 Possible solution
– Recombination of models

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 Abstract

Paul A Bates – Modelling Procedure

 Define domains
 Make models (FAMS/Pmodeller/EsyPred3D)
– Manual inspection/correction of alignments
– Alignment of annotated residues (PFAM)
– Preferably use alignment with >2 bits/aa
 Select pair of models
– Superimpose
– Crossover or mutate (average coordinates)
 Select best proportion
– Contact pair potentials
– Solvation energies (calculated from solvent accessible area)
 Convergence
– Minimization and final refinements OL
 Abstract

Barry Honig

 Sequence&structure profile-profile based alignment

– Database of template profiles
 Multiple structure alignment
 Sequence based profiles
 Position specific gap penalties derived from secondary
structure
 Calibration to estimate statistical significance
– Query profile
 Sequence based profile
 Predicted secondary structure (consensus between PSI-
PRED,PHD,JNET)

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 Abstract

Ying Xu

 PROSPECT:optimal alignments for a given

energy function with any combination of the
following terms:
1. mutation energy (including position-specific score
matrix derived from multiple-sequence
alignments),
2. singleton energy (including matching scores to
the predicted secondary structures),
3. pairwise contact potential
4. alignment gap penalties.
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 Abstract

Gilles Labesse

 Meta Server
– 3D-PSSM, PDB-BLAST, FUGUE,
GenTHREADER, SAM-T99, JPRED-2
 Tool for Incremental Threading optimization
(T.I.T.O.)
 Consensus ranking

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LiveBench

 The Live Bench Project is a continuous

benchmarking program. Every week
sequences of newly released PDB proteins
are being submitted to participating fold
recognition servers. The results are collected
and continuous evaluated using automated
model assessment programs. A summary of
the results is produced after several months
of data collection. The servers must delay the
updating of their structural template libraries
by one week to participate. OL
Meta Server

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 http://bioinfo.pl/meta/target.pl?id=7296

Meta Server

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Score # wrong
# correct

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Best servers?
 FFA3
 3DS5
 INBG
 SHUM
 3DPS
 3DS3
 FUG3
 SHGU
 FUG2
 PCO2
 PRO2
 MGTH
 SFPP
 PMO3 OL
Links to fold recognition servers
 Databases of links
– http://bioinfo.pl/meta/servers.html
– http://mmtsb.scripps.edu/cgi-bin/renderrelres?protmodel
 Meta server
– http://bioinfo.pl/meta/ (Example: http://bioinfo.pl/meta/target.pl?id=7296 )
 3DPSSM – good graphical output
– http://www.sbg.bio.ic.ac.uk/servers/3dpssm/
 GenTHREADER
– http://bioinf.cs.ucl.ac.uk/psipred/
 FUGUE2
– http://www-cryst.bioc.cam.ac.uk/~fugue/prfsearch.html
 SAM
– http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html
 FOLD
– http://fold.doe-mbi.ucla.edu/
 FFAS/PDBBLAST
– http://bioinformatics.burnham-inst.org/ OL