Parameter Value Description ref.
aful Archaeoglobus fulgidus [1-3]
mjan Methanococcus jannaschii
mthe Methanobacterium thermoautotrophicum
phor Pyrococcus horikoshii
scer Saccharomyces cerevisiae
cele Caenorhabditis elegans
aaeo Aquifex aeolicus
syne Synechocystis sp.
ecol Escherichia coli
bsub Bacillus subtilis
mtub Mycobacterium tuberculosis
hinf Haemophilus influenzae Rd
hpyl Helicobacter pylor
mgen Mycoplasma genitalium
mpne Mycoplasma pneumoniae
bbur Borrelia burgdorferi
tpal Treponema pallidum
ctra Chlamydia trachomatis
cpne Chlamydia pneumoniae
rpro Rickettsia prowazekii
Absolute Expression Expt.
vegsam GeneChip mRNA expression analysis of 6200 yeast ORFs under vegetative growth conditions. [4]
vegyou GeneChip mRNA expression analysis of 5455 yeast ORFs under vegetative growth conditions. [5]
sage mRNA expression analysis of 3788 yeast ORFs determined by  Serial Analysis of Gene Expression. [6]
matea GeneChip mRNA expression analysis of yeast mating type a strain grown on glucose. [7]
mateal GeneChip mRNA expression analysis of yeast mating type alpha strain grown on glucose.
gal GeneChip mRNA exprssion analysis of yeast mating type a strain grown on galactose.
heat GeneChip mRNA analysis of yeast mating type a strain grown on glucose at 30 degree before a 39 degree heat shock.
ref Reference transcriptome. This is a scaling and merging of the above experiments. [8]
Microarray Expt.
r =
cdc28 cDNA microarray genome-wide characterization of mRNA transcript levels during the cell cycle of a temperature sensitive CDC28 mutant yeast strain. [9]
cdc15 cDNA microarray genome-wide characterization of mRNA transcript levels during the cell cycle synchronized via a temperature sensitive CDC15 mutant yeast strain
alpha Analysis using cDNA microarrays of yeast mRNA levels after synchronization of cell cycle via alpha arrest factor
diaux Genome-wide cDNA microarray analysis of the temporal program of yeast mRNA expression accompanying the metabolic shift from fermentation to respiration [10]
spor cDNA microarray genome-wide analysis to assay changes in gene expression during sporulation. [11]
heatec cDNA microarray experiment and analysis on 4290 E.coli ORFs after exposure of the bacteria to heat shock. [12]
deve Analysis of genome wide changes during successive larval stages using cDNA microarrays of ~12000 C. elegan ORFs. [13]
Pair set
all All pairs within a PART included in the calculations in Wilson et al. (For example, for fold rankings this would be the total number of pairs within a fold.) [14]
foldonly A subset of the pair-set "all" that only includes pairs between structures that are in the same PART but different sub-PART. (If PART is fold, then sub-PART is superfamily; If PART is superfamily, then sub-PART is family.)
Amino Acid
  Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr. [15]
Data set
pdb100 All structures within a fold (as defined by SCOP pdb100d) [15]
pdb40 Similar to pdb100 but now using a version of the PDB clustered at 40% similarity (as defined by SCOP pdb40d)
Interaction type
pdball Interactions for a PART are computed with all other PARTS in the PDB databank [16,17]
pdba A subset of "pdball". Interactions for a PART are computed just with all-alpha proteins (SCOP class 1) in the PDB.
pdbb Similar to "pdba" but now just with all-beta proteins (SCOP class 2).
pdbab Similar to "pdba" but now just with mixed helix-sheet proteins (SCOP class 3 and 4)
scerall Interactions for a PART are computed with all other PARTS based on the yeast two-hybrid experiment [16-18]
scera Similar to "pdba" but now for yeast experiment
scerb Similar to "pdbb" but now for yeast experiment
scerab Similar to "pdbab" but now for yeast experiment
Interaction restriction
inter The interaction must occur between PARTS in different chains [16-18]
intra The interaction must occur between PARTS in the same chain.
none The union of "inter" and "intra". Interactions can occur in PARTS on the same or different chains.
Motion statistic
nresidue number of residues [19,20]
maxcadev Maximal displacement of an CA atom, in angstroms, of any residue during the motion (after fitting on the first core).
rmsoverall Overall RMS of two structures after they are superimposed by a sieve-fit technique. Note that they are larger than traditionally used RMS (details see ref.).
nhinges Number of hinges involved in the motion.
kappa The rotation (in degrees) around the screw axis necessary to superimpose two domains of motion.
transe Transition energy of the motion (maximum energy less minimum energy in motion) (in kcal/mole).
deltae Absolute value of energy difference between the "starting" and "ending" conformations of a motion (in kcal/mole).
Motion dataset
goldstd list of "gold-standard" motions ~220 [19,20]
auto list of ~4000 conformational different proteins based on analyzing the SCOP database for similar proteins with large RMS conformation differences between close sequence similarity
Transposon conditions
caff YPD + 8mM caffeine [21]
cyss Cyclohexmide hypersensitivity: YPD + 0.08 mgml-1 cycloheximide at 300C
wr White/red colour on YPD
ypg YPGlycerol
calcs Calcofluor hypersensitivity: YPD+12mgml-1 calcoluor at 300C
hug YPD + 46mgml-1 hygromycin at 300C
sds YPD + 0.003%SDS
bens Benomyl hypersensitivity: YPD + 10mgml-1 benomyl
bcip YPD + 5-bromo-4-chloro-3-indolyl phosphate at 370C
mb YPD + 0.001% methylene blue at 300C
benr Benomyl resistance: YPD + 20mgml-1 benomyl
ypd37 YPD at 370C
egta YPD + 2mM EGTA
mms YPD + 0.008% MMS
hu YPD + 75mM hydroxyurea
ypd11 YPD at 110C
calcr Calcofluor resistance: YPD + 0.3mgml-1 calcofluor at 300C
cycr Cyclohexmide resistance: YPD + 0.3mgml-1 cycloheximide
hhig Hyperhaploid invasive growth mutants
nacl YPD + 0.9M NaCl
Misc. quantities
pseu Number of pseudogenes in ribbon worm matching a particular PART [22]
func Total number of functions associated with this PART. (In this survey all non-enzyme functions were lumped into a single category.) [23]
enz Total number of enzymatic functions associated with this PART.
size Average length of a PART.  
age The year of the first structural determined.  

  • 1. Hegyi, H., Lin, J., Gerstein, M. (2000) submitted.
  • 2. Gerstein, M. (1998) Proteins, 33, 518-534.
  • 3. Gerstein, M., Levitt, M. (1997) Proc. Natl. Acad. Sci. USA, 94, 11911-11916.
  • 4. Jelinsky, S. A., Samson, L.D. (1999) Proc. Natl. Acad. USA., 96, 1486-1491.
  • 5. Holstege, F. C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C. J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. (1998) Cell, 95, 717-728.
  • 6. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E., Jr, Hieter, P., Vogelstein, B., Kinzler, K.W.,. (1997) Cell, 88, 243-251.
  • 7. Roth, F. P., Hughes, J. D., Estep, P.W., Church, G. M. (1998) Nature Biotechnology, 16, 939-945.
  • 8. Jansen, R., Gerstein, M. (2000) Nucleic Acids Res., 28, 1481-1488.
  • 9. Spellman, P. T., Sherlock, G., Zhang, M.Q., Iyer, V.R.,, Anders, K. Eisen, M.B., Brown, P.O., Botstein, D., Futcher, B. (1998) Mol Biol Cell, 9, 3273-3297.
  • 10. DeRisi, J. L., Iyer, V.R., and Brown P.O. (1997) Science, 278, 680-686.
  • 11. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O., Herskowitz, I. (1998) Science, 282, 699-705.
  • 12. Richmond, C. S., Glasner, J.D., Mau, R., Jin, H., Blattner, F.R. (1999) Nucleic Acids Res., 27, 3821-3835.
  • 13. Wixon, J., Blaxter, M., Hope, I., Barstead, R., Kim, S. (2000) Yeast, 17, 37-42.
  • 14. Wilson, C. A., Kreychman, J., Gerstein, M. (2000) J. Mol. Biol., 297, 233-249.
  • 15. Brenner, S. E., Koehl, P., Levitt, M. (2000) Nucleic Acids Res., 28, 254-256.
  • 16. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T., Chothia, C. (1998) J. Mol. Biol., 284, 1201-1210.
  • 17. Teichmann, S., Chothia, C., Church, G., Park, J. (2000) Bioinformatics, 16, 117-124.
  • 18. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., Rothberg, J.M. (2000) Nature, 403, 623-627.
  • 19. Gerstein, M., Krebs, W. (1998) Nucleic Acids Res., 26, 4280-4290.
  • 20. Krebs, W., Gerstein, M. (2000) Nucleic Acids Res., 28, 1665-1675.
  • 21. Ross-Macdonald, P. C., P.S.R., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K., Sheehan, A., Symoniatis, D., Umansky, L., Heidtman, M., Nelson, F.K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G.S., Snyder, M. (1999) Nature, 402, 413-418.
  • 22. Harrison, P., Echols, N., Gerstein, M. (2000) submitted.
  • 23. Hegyi, H., Gerstein, M. (1999) J. Mol. Biol., 288, 147-164