Structural Classification of Proteins




Class: Alpha and beta proteins (a+b)
- Mainly antiparallel beta sheets (segregated alpha and beta regions)
Lineage:
- Root: scop
- Class: Alpha and beta proteins (a+b)
Mainly antiparallel beta sheets (segregated alpha and beta regions)
Folds:
- Microbial ribonucleases (1)


single helix packs against antiparallel beta-sheet
- Lysozyme-like (1)

common alpha+beta motif for the active site region
- Cysteine proteinases (1)


consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
- His-Me finger endonucleases (1)

core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
- RNase A-like (1)


contains long curved beta-sheet and 3 helices
- Prion protein domain (1)

beta-alpha-beta-alpha(2); antiparallel beta-ribbon
- LysM domain (1)

beta-alpha(2)-beta;
- Urease, gamma-subunit (1)

alpha(3)-beta(2); antiparallel hairpin
- IL8-like (2)


beta(3)-alpha
- DNA-binding domain (1)

beta(3)-alpha; 2 layers: alpha/beta
- Penicillin-binding protein 2x (pbp-2x), c-terminal domain (1)

alpha1-beta3; 2 layers: alpha/beta; order 132
- Ribosomal proteins L23 and L15e (1)

beta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet: order 1243
- HIT-like (1)

alpha-beta3-alpha-beta2; 3 layers: alpha/beta/alpha
- Ribosomal protein S5 domain 2-like (1)

core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
- beta-Grasp (ubiquitin-like) (9)


core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
- FAD-linked reductases, C-terminal domain (1)


alpha+beta sandwich
- Cystatin-like (5)


Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
- Transcriptional coactivator PC4 C-terminal domain (1)

beta(4)-alpha; forms dimers by swapping helices
- MHC antigen-recognition domain (1)


dimeric
- Ubiquitin conjugating enzyme (1)

alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2
- Diaminopimelate epimerase (1)

mixed beta-sheet folds into a barrel (n=8, S=14) around the central helix
- Fluorescent proteins (1)

beta-sheet folds into a barrel (n=11, S=14) around the central helix
- Transcriptional factor tubby, C-terminal domain (1)

beta-sheet folds into a barrel (n=12, S=12) around the central helix
- Pilin (1)

contains very long N-terminal helix, which end is packed against beta-sheet
- Acidic mitochondrial matrix protein p32 (1)

core: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coil subdomain
- FKBP-like (3)

core: beta(2)-alpha-beta(2); antiparallel beta-sheet
- Ribosomal protein S16 (1)

beta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234
- Ribosomal protein S19 (1)

alpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123
- Ribosomal protein L31e (1)

beta-alpha-beta-(aplha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 1342
- Allophycocyanin linker chain (domain) (1)

beta(2)-alpha-beta; 2 layers: alpha/beta
- Cdc48 domain 2-like (1)

beta-alpha-beta(3); 2 layers: alpha/beta
- Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (1)

beta-alpha-beta(3); 2 layers: alpha/beta
- Bacterial protein-export protein SecB (1)

beta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432
- DNA-binding domain of Mlu1-box binding protein MBP1 (1)

beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
- Heme-binding protein A (HasA) (1)

beta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432
- Chalcone isomerase (1)

beta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order 1234567
- CBS-domain (1)

core: beta-alpha-beta(4); 2 layers: alpha/beta
- Thioesterase/thiol ester dehydrase-isomerase (1)

core: beta-alpha-beta(4); 2 layers: alpha/beta
- Dynein light chain 8 (DLC8) (1)

core: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 1342
- CI-2 family of serine protease inhibitors (1)


alpha+beta sandwich; loop across free side of beta-sheet
- alpha/beta-Hammerhead (5)

core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
- POZ domain (1)

core: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
- Elongation factor Ts (EF-Ts), dimerisation domain (1)

beta(2)-alpha(n)-beta; 2 layers a/b; antiparallel sheet: 123
- Fe,Mn superoxide dismutase (SOD), C-terminal domain (1)


alpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213
- Ribosomal protein L7/12, C-terminal domain (1)

beta-alpha(2)-beta-alpha-beta; 2 layers, alpha/beta
- Transcription-state regulator AbrB, the N-terminal DNA recognition domain (1)

beta-alpha-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
- Ribosomal protein L11, N-terminal domain (1)

beta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
- Anti-LPS factor/recA domain (2)


alpha-beta(3)-alpha(2); 2 layers, alpha/beta
- Signal recognition particle alu RNA binding heterodimer, SRP9/14 (1)

(beta)-alpha-beta(3)-alpha; 2 layers, alpha/beta
- dsRBD-like (3)

alpha-beta(3)-alpha; 2 layers: alpha/beta
- KH-domain (1)

beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
- Alpha-lytic protease prodomain-like (3)

core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
- Ribosomal protein S3 C-terminal domain (1)

alpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143
- Enolase N-terminal domain-like (1)

beta(3)-alpha(3); meander and up-and-down bundle
- Ribosomal protein L22 (1)

beta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domain fold by a circular permutation
- GroEL-like chaperone, intermediate domain (1)


3-helical bundle packed against 3-stranded mixed beta-sheet
- DNA damage-inducible protein DinI (1)

beta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loops
- Ferredoxin-like (36)


alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
- Ribosomal protein L30p/L7e (1)

core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity with the ferredoxin-like fold
- Probable bacterial effector-binding domain (1)

duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12)
- tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase (1)

duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
- Pepsin inhibitor-3 (1)

duplication of beta(3)-alpha(2) motif: meander beta sheets form barrel-like structure
- mRNA triphosphatase CET1 (1)

duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
- eIF1-like (1)

beta(2)-alpha-beta(2)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet: order 51243
- Hedgehog/DD-pepidase (1)

alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
- Alpha-L RNA-binding motif (1)

alpha(2)-beta(2)-loop-beta; 2 layers: alpha/beta
- RRF/tRNA synthetase additional domain-like (3)

core:alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
- IF3-like (2)

beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
- C-terminal domain of TolA (1)

alpha-beta(2)-alpha-beta; 2 layers, alpha/beta; left-handed beta-alpha-beta unit
- Yest killer toxins (1)

beta-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta; left-handed crossover connection
- Cell division protein MinE topological specificity domain (1)

dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
- Cyanase C-terminal domain (1)

intertwined dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
- RuBisCO, small subunit (1)

alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
- DCoH-like (4)

beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
- MutS N-terminal domain-like (2)

beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
- GYF domain (1)

beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
- Ribosomal protein L5 (1)

beta-alpha-beta(2)-alpha-beta(3)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet: order 231654
- RPB5-like RNA polymerase subunit (1)

core: beta-alpha-beta-alpha-beta(2); 2 layers, alpha/beta
- Bacillus chorismate mutase-like (4)

core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
- Tautomerase/MIF (1)

(beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet
forms trimers with three closely packed beta-sheets
- Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (1)


core: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
- N domain of copper amine oxidase-like (2)

alpha-beta(5)-alpha; 2 layers: alpha/beta; meander antiparallel sheet
- Bactericidal permeability-increasing protein, BPI (1)

beta-alpha-beta(5)-alpha-beta2; 2 layers: alpha/beta; antiparallel sheet
- Subtilisin inhibitor (1)

alpha+beta sandwich
- RNA bacteriophage capsid protein (1)

6-standed beta-sheet followed with 2 helices; meander
- Translation initiation factor eIF4e (1)

beta(2)-alpha-beta(2)-alpha-beta(2)-alpha-beta-2; 2 layers: alpha/beta; antiparallel sheet: 21356478
- CO dehydrogenase flavoprotein C-domain-like (2)


core: beta(3,4)-alpha(3); alpha+beta sandwich
- SRF-like (1)

alpha-beta(2)-alpha; dimer; 3 layers a/b/a; antiparallel beta-sheet
- The origin DNA-binding domain of SV40 T-antigen (1)

alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers:a/b/a; antiparallel sheet 41325
- NADH oxidase/flavin reductase (1)

core: (alpha-beta-alpha-beta)2; 3 layers a/b/a; antiparallel beta-sheet: 1243
- N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 (1)

alpha-beta-alpha(2)-beta(3)-alpha; 3 layers a/b/a; antiparallel beta-sheet: 4123
- Zincin-like (2)

contains mixed beta sheet with connection over free side of the sheet
- SH2-like (1)


3 layers: a/b/a; antiparallel beta-sheet of 5 strands is flaked by two helices
- Histidine-containing phosphocarrier proteins (HPr) (1)


beta-alpha-beta(2)-alpha-beta-alpha; 2 layers: a/b; antiparallel sheet 1423
- Homing endonuclease-like (2)

alpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
- T-fold (1)

beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234
tunnel-shaped: its known members form wide oligomeric barrels different sizes
- Cell cycle regulatory proteins (1)

beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243
can form strand-exchange dimers
- beta-lactamase-inhibitor protein, BLIP (1)

alpha(2)-beta(4); 2 layers: alpha/beta
- Ribosomal protein L9 C-domain (1)

alpha-beta-alpha(2)-beta(2); 2 layers: alpha/beta
- L9 N-domain-like (1)

beta(2)-alpha-beta-alpha; 3 layers: alpha/beta/alpha
- Polynucleotide phosporylase/guanosine pentaphospate synthase (PNPase/GPSI), domains 2 and 5 (1)

beta(2)-alpha-beta(2)-alpha; 3 layers: alpha/beta/alpha; antiparallel sheet: order 2134
- Regulatory factor Nef (1)

alpha(2)-beta(4)-alpha; 3 layers: alpha/beta/alpha
- Mosquitocidal delta-endotoxin CytB (1)

core: beta-alpha(2)-beta-alpha(2)-beta(4); 3 layers: a/b/a
- Class II aaRS and biotin synthetases (1)


contains large mixed beta-sheet
- Clathrin adaptor appendage domain (1)

beta-alpha-beta-alpha-beta(4)-alpha; 3 layers: a/b/a; bifurcated antiparallel beta-sheet
- Sterol carrier protein 2 (SCP2) (1)

alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
- Ran-binding protein mog1p (1)

(beta-hairpin)-beta(3)-alpha-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet of 7 strands; order: 1237654
- Acyl-CoA N-acyltransferases (Nat) (1)

3 layers: a/b/a; contains mixed beta-sheet
- Actin depolymerizing proteins (1)

3 layers: a/b/a; contains mixed beta-sheet
- Profilin-like (3)

core: 2 alpha-helices and 5-stranded sheet; 3 layers: alpha/beta/alpha
- PR-1-like (1)

alpha-beta-alpha-beta-alpha(2)-beta(2); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
- IIA domain of mannitol-specific and ntr phosphotransherase EII (1)

beta-alpha(2)-beta(3)-alpha(3); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
- Nucleoside triphosphate pyrophosphorylase (MutT) (1)

beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
contains beta-grasp motif
- 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain (1)

core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
- Hypothetica protein YrdC (1)

core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta(3); 3 layers; mixed twisted sheet of 9 strands
- Hypothetica protein HI1434 (YbaK homologue) (1)

core: alpha-beta-alpha-beta(2)-(alpha-beta)2-alpha-beta(2)-alpha-beta; 3 layers; bifurcated mixed sheet
- Thymidylate synthase/dCMP hydroxymethylase (1)

contains large mixed beta-sheet
- Bacteriophage T7 lysozyme (Zn amidase) (1)

contains mixed beta-sheet
- Streptomyces lysozyme (1)
contains curved mixed beta-sheet; incomplete barrel
- Cytochrome b5 (1)

small, heme-binding fold
- DNA topoisomerase I domain (1)

beta(2)-alpha-beta-(alpha)-beta(2); left-handed crossover between strands 2 & 3
- ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (1)

8-stranded mixed beta-sheet; 2 layers: alpha/beta
- Sporulation responce regulatory protein Spo0B (1)

core: alpha-beta-alpha-beta(2)-(alpha)-beta(2)
- Ribonuclease Rh-like (1)

alpha+beta fold
- Ornithine decarboxylase C-terminal domain (1)

complex alpha+beta motif
- Pentein, beta/alpha-propeller (1)

duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
- Creatinase/aminopeptidase (1)


duplication: composed of two very similar alpha+beta folds
- Glutamine synthase/guanidino kinase catalytic domain (1)


- TBP-like (3)

beta-alpha-beta(4)-alpha
- S-adenosylmethionine synthetase (1)


duplication: consists of 3 similar intertwined domains
structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
- DNA clamp (1)


contains two helices and two beta sheets
duplication: fold has internal pseudo two-fold symmetry
- Mitochondrial processing peptidase, MPP (1)

beta(2)-alpha(2)-beta(2)-alpha(5)-beta; 2 layers: a/b; mixed sheet: order 15243: strands 2 to 5 are connected with a ferredoxin-like topology
- Molybdemum cofactor-binding domain (1)

beta(2)-alpha-beta-alpha-beta; 2 layers: a/b; mixed sheet: order 1243: crossing loops
- Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 (1)

beta-alpha-beta-alpha-beta(3)-alpha(2,3); mixed sheet: order 12345; left-handed crossover connection bettween strands 2 and 3
- The spindle assembly checkpoint protein mad2 (1)

beta-alpha(2)-beta(2)-alpha-beta(3); mixed sheet: order 132465
- Phospholipase D/nuclease (1)

beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
- Monooxygenase (hydroxylase) regulatory protein (1)

corner-like structure formed by two sheets and filled in with 2-3 helices
- B3/B4 domain of PheRS, PheT (1)

3 layers: beta/beta/alpha sandwich
- Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain (1)

3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
- Ribosomal protein S8 (1)

consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a
- Ribosomal protein L6 (1)

consists of two beta-sheets and one alpha-helix packed around single core
- ATP-grasp (2)

Consists of two subdomains with different alpha+beta folds
shares functional and structural similarities with the PIPK and protein kinase superfamilies
- SAICAR synthase-like (1)

consists of two alpha+beta subdomains
- Protein kinase-like (PK-like) (1)

consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
- FAD-binding domain (1)

consists of two alpha+beta subdomains
- Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain (1)

consists of two alpha+beta subdomains
- Methenyltetrahydromethanopterin cyclohydrolase (1)

consists of two alpha+beta subdomains
- Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap) (1)

consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit
- Nitrile hydratase alpha chain (1)

4 layers a/b/b/a; inside is a sandwich of two 2-stranded beta-sheets
- 4'-Phosphopantetheinyl transferase SFP (1)

4 layers a/b/b/a; duplication of beta-alpha(3)-beta(2) motif
- DNase I-like (1)


contains beta-sandwich; duplication of alpha+beta motif
- Aldehyde ferredoxin oxidoreductase, N-terminal domain (1)

contains sandwich; duplication of alpha+beta motif with single mixed sheet
motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
- N-terminal nucleophile aminohydrolases (Ntn hydrolases) (1)

4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
- L-aminopeptidase D-Ala-esterase/amidase (1)

duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
- Histidine decarboxylase (1)

contains "silk" beta-sandwich flanked on both sides with alpha-helices
- S-adenosylmethionine decarboxylase (1)

duplication of beta-alpha-beta(4)-alpha-beta-alpha-beta(2) motif; 4 layers a/b/b/a; antiparallel beta-sheets: order 23451687
- Metallo-hydrolase/oxidoreductase (1)

duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets
- Protein serine/threonine phosphatase 2C (1)

4 layers: alpha/beta/beta/alpha; antiparallel beta sheets
- Metallo-dependent phosphatases (1)

4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
- Nitrilase/N-carbamyl-D-aminoacid amidohydrolase (1)

4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
- Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit TrpE (1)

duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
- Lactate & malate dehydrogenases, C-terminal domain (1)


unusual fold, defines family
- DNA breaking-rejoining enzymes (1)

core: alpha3-beta3-alpha4; one side of beta-sheet is exposed
- SMAD MH1 domain (1)

consists of four alpha-helices and three beta-ribbons
- Ribosome inactivating proteins (RIP) (1)


contains mixed beta-sheet
- ADP-ribosylation (1)


unusual fold
- Peptide deformylase (1)

alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
- Succinate dehydrogenase/fumarate reductase catalytic domain (1)

unusual fold
- C-type lectin-like (1)

unusual fold
- SRCR-like (2)

unusual fold; disulphide-rich; core: beta-x-alpha-beta-loop-beta
- Fibrinogen C-terminal domains (1)

unusual fold
- gp120 core (1)

unusual fold
- Methionine synthase (activation domain) (1)

unusual fold
- Nitric oxide (NO) synthase oxygenase domain (1)

unusual fold
- Penicillin-binding protein 2x (pbp-2x), N-terminal domain (1)

unusual fold
- Sulfite oxidase, middle catalytic domain (1)

unusual fold; contains 3 layers of beta-sheet structure and a beta-grasp like motif
- Fumarylacetoacetate hydrolase, FAH (1)

unusual fold; contains 3 layers of beta-sheet structure and a SH3-like like motif
- Aromatic aminoacid monoxygenases, catalytic and oligomerization domains (1)

unusual fold
- Substrate-binding domain of HMG-CoA reductase (1)

unusual fold
- Conserved core of transcriptional regulatory protein vp16 (1)

unusual fold
- Insert subdomain of RNA polymerase alpha subunit N-terminal domain (1)

unusual fold; contains a left-handed beta-alpha-beta unit
- Baseplate structural protein gp11 (1)

unusual fold; trimer
- Major capsid protein gp5 (1)

unusual fold
- Non-globular alpha_beta subunits of globular proteins (1)

Generated from scop database 1.55 with scopm 1.095 on Mon Jul 9 18:35:50 2001
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© 1994-2001 The scop authors /
scop@mrc-lmb.cam.ac.uk