Datasets compiled from literature (Collection of existing datasets)

We collected and compilied following datasets from literature. In past, these datasets have been used for developing prediction methods. This list is not complete, collection is in progress, please help us by submitting/suggesting new dataset to this collection

Table: Showing list of Datasets compiled from published literature

Types of Datasets	Sub Types	PDB chains in dataset	References (Pubmed ID)	Original site	Download Data
Regular Secondary structure	helix, strand, coil	513,406 1155 24761 60,21 987,988 83	25883141 29501620 25380779 28968641 23298369 22095872	Jpred4 PATSIM POLYPROLINE MemBrain SSCon K2D3	CB513 , CB406 PATSIM PolyprOnline MemBrain SSCon K2D3(Table S1)
	Strand	1452	24064422	bcov	BetaSheet1452
Irregular Secondary structure	Beta-Turns	1296 547 426 426,6376,20142	20673368 15822097 12592033 25728793	DEBT COUDES BTEVAL BetaTPred3.0	PDB1296 FA547 GR426 BT426,BT6376,BT20142
	Gamma-Turns	490 749 320	17936305 12662358 10878855	sciencedirect wiley.com JBIOSCI	PA490 KG749 KG320
	Alpha-Turns	490 193	16894602 8652792	Alpha Turn V1.0 wiley.com	JX490 VP193
	B-Hairpin	534	12177429	BhairPred	BhairPred
	Beta barrel	1881712	22843985	TMBB-DB	TMBB-DB
PDB derived Datasets with non-redundant sequence and structural quality criteria	PDB_SELECT	5130	19783827	PDB_SELECT	PDB_SELECT_25
	PDBFINDER	168357	9021272	PDBFINDER	PDBFINDER
	PISCES	3023	12912846	PISCES	PISCES
	AbDb	1476 complete non-redundant, 57 non-redundant light chains, 177 non-redundant heavy chains	29718130	AbDb	AbDb
DNA/RNA interacting residues	DNA	206 500 62 25 782 488,82	21069866 19767616 16845003 19594868 28381244 28132027	Proteins 3dfootprint BindN BindN DisBind DRNAPred	DBP206 3D-footprint PDNA-62 PRINR25 DisBind DRNAPred
	RNA	147 205 109 782 488,82	17483510 20483814 16790841 28381244 28132027	PRIDB PRNA RNABindR DisBind DRNAPred	RB147 PRNA MT109 DisBind DRNAPred
DNA/RNA interacting proteins	DNA	146 1153 92 146	18042272	DNAbinder	Main Dataset Alternate Dataset Realistic Dataset Independent Dataset
	RNA	377 766,326 26306,24228,1678,2662 2241,369 1678	20677174 26607710 29495575 22192482 22192482	RNApred PRIdictor RPiRLS RPISeq RPIntDB	RNA Binding Data non-RNA binding data PRIdictor data RPiRLS data RPISeq data RPIntDB data
Nucleotide interacting residues	ATP	168 429 168,227 227,17,1372	20021687 29361215 23288787 22130595	ATPint ATPbind TargetATPsite NsitePred	ATPint168 ATPbind TargetATPsite NsitePred_ATP
	ADP	321,25,1372	22130595	NsitePred	NsitePred_ADP
	AMP	140,18,1372	22130595	NsitePred	NsitePred_AMP
	GTP	44 56,6,1372	20525281 22130595	GTPBinder NsitePred	GTPbinder44 NsitePred_GTP
	GDP	105,9,1372	22130595	NsitePred	NsitePred_GDP
	NAD	195	20353553	NADbinder	NADbinder195
	FAD	198	20122222	FADPred	FADPred198
Metals and Ions Interacting Residue	Ioncom dataset	142(Zn), 110(Cu), 227 (Fe2+), 103 (Fe3+), 379(Mn), 179 (Ca), 103(Mg), 53(K), 78(Na), 62(CO3), 22(NO2), 303(So4), 339(Po4)	27378301	IonCom	IonCom_dataset
Bacterial protein interaction	Functional interaction	1941 229 79	19798435 22102573 22053087	Bacteriome DBETH MimoDB	Functional interactions dataset DBETH MimoDB
	TAP interaction	918	19798435	Bacteriome	Hu et al. TAP interaction dataset
	Functional & TAP interaction	2283	19798435	Bacteriome	Combined interactions dataset
	Experimental interaction	2291	19798435	Bacteriome	Extended interaction dataset
Protein crystalization	Propensity Dataset1	3958	18285371	SSPF Crystallisation Propensity Predictors (Main server non-functional)	ParCrys Datasets
	Propensity Dataset2	144, 500	19755114	MetaPPCP (Main server non-functional)	MetaPPCP Datasets
	Protein crystallization, purification and production propensity dataset 1	3587, 3585	21685077	PPCpred	PPCpred Dataset
	Protein crystallization, purification and production propensity dataset 2	5383, 23348	25148528	PredPPCrys (Main server non-functional)	PredPPCrys Dataset
	Protein crystallization, purification and production propensity dataset 3	5383, 23348, 11946	26906024	Crysalis	Crysalis Dataset
	Protein crystallization and propensity dataset	1197, 2378	24019868	SCMCRYS (Main server non-functional)	SCMCRYS Dataset
Helix packing	Helix packing	610	wiki.c2b2	Helix packing patterns	Helix packing dataset
Membrane proteins	Homologous Membrane Proteins	36	16648166	HOMEP	homep datasets
	Transmembrane Proteins	247	15111065	Phobius	Phobius
	Membrane Proteins	3249 trainset,4333 testset,7695 non-membrane proteins	22386149	ProClusEnsem	ProClusEnsem
Dihedral angles	Dihedral angles dataset	513,80,175,179,212,1989,1988	20025785	DISSPred	disspred datasets
	Protein backbone dihederal angles	1267,1267,85,40,5046	29745828	RaptorX-Angle	RaptorX-Angle datasets
	Dihedral angles from chemical shifts and/or homology	141,31,15	16845087	PREDITOR	PREDITOR datasets
	Protein Backbone Torsion Angle	500,460,1029	18923703	ANGLOR	ANGLOR datasets
	Protein Torsion Angle	1552,11	28923002	DNTor	DNTor datasets
Surface accessibility	Surface accessibility dataset	215	11170200	Protein surface accessibility	Manesh-215
	AcconPred	5729,945	26339631	Solvent Accessibility and Contact Number Simultaneously	AcconPred
Rotamer Libraries	Dunbrack Rotamer Libraries	850	12163064	Dunbrack Rotamer Libraries	Dunbrack Rotamer Libraries
	Tuffery et al's rotamer libraries	2926	12557186	Backbone independent Backbone Dependent	Tuffery's Backbone independent Tuffery's Backbone dependent
	Penultimate Rotamer Library	240	10861930	Penultimate Rotamer Library	Penultimate Rotamer Library
	Kirys et al's Rotamer Library	233	22544766	Kirys Rotamer Library	Kirys Rotamer Library (Only Table S2&S3)