CAPRI

Critical Assessment of Prediction of Interactions

CAPRI docking targets

• CAPRI-01 (unbound/unbound) Lactobacillus HPr kinase - B. subtilis HPr

• CAPRI-02 (unbound/bound) bovine rotavirus VP6 - Fab

• CAPRI-03 (unbound/bound) flu hemagglutinin - Fab HC63

capri1 capri2 capri3

Docking Algorithms Flow

Molecular Surface representation

Critical points selection

Matching of critical points

Clustering and Scoring

Active site knowledge

Molecular Surface RepresentationBudda• Connoly surface for

grid distance function calculations

• Shuo points as critical points

Kely• Connoly surface as

critical points

Critical Points SelectionBudda• Volume function is

computed for each shuo point and knobs and holes are selected.

Kely• Volume function is

computed for each point and local minimum and maximum of knobs and holes are selected.

Matching of Critical PointsBoth algorithms use Pose-Clustering technique:• For each triangle of receptor compute the

transformation to each ligand matching triangle.• Cluster transformations.• Score the results.

Complexity: O(m3n3)

Reference Frame Selection

Budda

• Each reference frame is defined by one critical point (knob, hole) and two it’s neighbors.

• The signature includes triangle sides length, the angles a1, a2 and torsion angle w for AB and AC.

Kely

• Each reference frame is defined by 2 points (knobs,holes) and their normals.

• The signature information includes the distance between two points, the angles a1, a2 and torsion angle w.

wa1 a2

A

B

C

Reference Frame Complementarity

Budda

• Knob matches hole for one point only, not necessary for neighbor points.

• The difference between distances (AB,AC,BC) < d_thr.

• The difference between the angles < angle_thr.

Complexity: O(m3n3)

Kely

• Knob matches hole for every point.

• The difference between distances < d_thr.

• The difference between the angles < angle_thr.

Complexity: O(m2n2)

wa1 a2A

B

C

ClusteringBudda• At first fast clustering

by transformation parameters is performed.

• For final results, the RMSD clustering on the interface is applied.

Kely• The transformations

are clustered by the rotational angle between every two conformers.

Geometric ScoringBudda

• A number of ranges on the surface of receptor molecule is defined:

< -2 |-2:-1.5|-1.5:-1| -1:1 |1:1.5| >1.5

• For each interface number of surface (shuo) points in each range is computed.

• The score is a weigted function of each layer.

• In addition, number of penetrating residues is computed and added to the score.

Kely

• Only 3 ranges are used:

Surface, Exterior, Core.

• The score is given as:

GS=S-4E-C2/(1+e6-C)

• Additional geom. score:

NS = GS/S

• Electrostatic “clashes” filter

• Connected components of interface filter.

Capri1: enzyme – inhibitor• HPr kinase/phosphatase is a key regulatory

enzyme controlling carbon metabolism in bacteria.• The protein is a hexamer.• HprK/P contains the Walker motif - characterisctic

of nucleotide-binding proteins

Capri1: enzyme – inhibitor

Capri1: enzyme – inhibitor

• It catalyses the ATP-dependent phosphorelation/dephosphorelation of Ser46 in HPr.

Capri1: enzyme – inhibitor• The docking was done using Walker motif and

Ser46 as active site, so that only relevant solutions could be created.

• The filter on the distance between phosphate and oxygen atoms of Asp was applied. Only relevant solutions were selected.

Capri 2 and Capri3- biology background

• Viral capsid:

biology background …

• Capri2 - VP6 protein of rotavirus that causes gastroenteritis in children.

• Capri3 – influenza hemagglutinin.

Capri 2

02antigen.pdb

Capri2 antigen ...

• Trimmer. (symmetry)• The surface of the B (helices) domain is buried in

rotavirus capsid.• The H-domain interacts with the antibody.• A ‘hint’ was given- to use the trimmer in the

docking, meaning that active site is expanded to more than one chain.

Capri 3

Raswin file

Capri3 antigen ...

• Hexamer. 3 dimmers (symmetry)• One chain of the dimmer(s) is buried in the capsid• Other antibody-antigen complexes of this antigen

also implies active site is in the ‘external’ chains (B,D and F)

Antibodies - CDRs

The antibody active site is always in the CDRs,

which are in the variable part of the antibody • CDRs H3 and L3 are

most likely to be in the

active site.• At least 4 CDRs in the

active site

CDRs location utility

• The light and heavy chain has conserved areas which enables us to align a given sequence to a consensus sequence which was built using statistical data.

• This alignment is then used to locate the CDRS area.

• This information may be used in docking programs, in the docking process itself (budda) or in a filtering process (kely).

Antibodies Tyr, Trp and Arg propensities

• Antibodies active sites have a high propensities of Tyr,Trp and Arg.

• This property may be used to filter out docking results or even be used in the scoring function. (we used both)

Symmetry

• Both antigens (and also the capri1 enzyme) have a rotational symmetry.

• ‘rmsd-like distance function’ Clusterring is used to gather transformations which are symmetrically similar.

Clustering different alg results

• Any algorithms performs well on some targets and less on other.

• Since 10 results should have been submitted to each target it seemed reasonable to gather results from different algorithms, re-score them, and then re-cluster them.

CAPRI Docking Flow

Molecular Surface representation

Critical points selection

Matching of critical points

Clustering and Scoring

• Compute Connolly and Shuo surface representation.

• Compute CDRs in case of Antibody-Antigen docking.

• Select knobs and holes for CDRs only

• Match critical points - use 2 points and their normals for faster matching.

• Cluster transforms.

• Compute geometric score.

• Apply CDRs, Tyr-Trp, NS, interface connectivity, symmetry filters.

RankBestRMSDComplexReceptorLigandDescription11.281CGI1CHG1HPTAlpha-chymotrypsinogen / Pancreatic secretory trypsin inhibitor11.221CHO5CHA2OVOAlpha-chymotrypsin / Ovomucoid 3rd Domain

352.832PTC2PTN6PTIBeta-trypsin / Pancreatic trypsin inhibitor11.691TGS2PTN1HPTTrypsinogen / Pancreatic secretory trypsin inhibitor

112.072SNI1SUP2CI2Subtilisin Novo / Chymotrypsin inhibitor 261.592SIC1SUP3SSISubtilisin BPN / Subtilisin inhibitor

101.651CSE1SCD1ACB(I)Subtilisin Carlsberg / Eglin C1112.372KAI2PKA6PTIKallikrein A / Trypsin inhibitor2921.731BRC1BRA1AAPTrypsin / APPI

1PPE*2PTN1PPETrypsin / CMT-11TAB*2PTN1TABTrypsin / BBI

20.7831ACB5CHA1CSE(I)Alpha-chymotrypsin / Eglin C21.571BRS1A2P1A19Barnase / Barstar

141.41MAH1MAA1FSCMouse Acetylcholinesterase / inhibitor11.551UGH1AKZ1UGIHuman Uracil-DNA glycosylase / inhibitor

1UDI*1UDH1UDIVirus Uracil-DNA glycosylase / inhibitor1STF*1PPN1STFPapain / Stefin B2TEC*1THM2TECThermitase / Eglin C4HTC*2HNT4HTCAlpha-Thrombin / Hirudin

32.051DFJ2BNH7RSARibonuclease inhibitor / Ribonuclease A12.271FSS2ACE1FSCAcetylcholinesterase / Fasciculin II61.951AVW2PTN1BA7Trypsin / Sotbean Trypsin inhibitor

Enzyme – inhibitor test set results (unbound)

Antibody-Antigen test set results (unbound/bound)

RankBest RMSDComplexReceptorLigandDescription11.261MLC1MLB1LZAIgG1 D44.1 Fab fragment / Lysozyme11.31FBI*1FBI1HHLIgG1 Fab fragment / Lysozyme

111.121WEJ1QBL1HRCIgG1 E8 Fab fragment / Cytochrome C11.371AHW1FGN1BOYAntibody Fab 5G9 / Tissue factor21.272JEL*2JEL1POHJel42 Fab Fragment / A06 Phosphotransferase11.141BQL*1BQL1DKJHyhel - 5 Fab / Lysozyme

2582.381DQJ1DQQ3LZTHyhel - 63 Fab / Lysozyme40.871JHL*1JHL1GHLIgG1 Fv Fragment / Lysozyme31.121BVK1BVL3LZTAntibody Hulys11 Fv / Lysozyme10.9491NCA*1NCA7NN9Fab NC41 / Neuraminidase

341.091NMB*1NMB7NN9Fab NC10 / Neuraminidase1MEL*1MEL1LZAVh Single-Domain Antibody / Lysozyme2VIR*2VIR2VIUIgg1-lamda Fab / Hemagglutinin

1911.71EO8*1EO82VIUBh151 Fab / Hemagglutinin

791.261QFU*1QFU2VIUIgg1-k Fab / Hemagglutinin

81.451FDL1FDL1LZAIgG1 Fab fragment / Lysozyme21.181VFB1VFB1LZAFv Fragment / Lysozyme21.123HFL3HFL5LYMIgg1 Fab Fragment (Hyhel-5) / Lysozyme

New classes and utilities

MoleculeGrid class - new class in GAMB++ library. The class can compute molecule grid with distance function, volume function and normals for critical points.

CDR utility - utility that finds CDRs for antibody, by aligning new sequence to consensus sequence.

Symmetry and Clustering utility

New docking version of budda - including new grid representation, two points and normals matching.