Parameter	Value	Description	ref.
Genome x=	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. e=	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 f=	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]
Pair set f=	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.)	[14]
Amino Acid a=		Ala, Cys, Asp, Glu, Phe, Gly, His, Ile, Lys, Leu, Met, Asn, Pro, Gln, Arg, Ser, Thr, Val, Trp, Tyr.	[15]
Data set p=	pdb100	All structures within a fold (as defined by SCOP pdb100d)	[15]
Data set p=	pdb40	Similar to pdb100 but now using a version of the PDB clustered at 40% similarity (as defined by SCOP pdb40d)	[15]
Interaction type y=	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 c=	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 s=	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 d=	goldstd	list of "gold-standard" motions ~220	[19,20]
Motion dataset d=	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	[19,20]
Transposon conditions b=	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 q=	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.	[23]
	size	Average length of a PART.
	age	The year of the first structural determined.

Reference:

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