Introduction

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WDSPdb 2.0

• WDSP database (created in 2014) is a free and comprehensive resource to provide high quality structural information of WD40 proteins as well as the featured sites. WDSPdb 2.0 has recorded about 600,000 predicted WD40 proteins from 4,426 species.
• It provided accurate structure predictions and featured sites annotations specifically for WD40 domains, based on the WDSP tool.
• It provided the general information of each WD40 protein and their cross-references linked to other well-known databases.
• It exhibited the 3D structure models for WD40 proteins whose repeat counts are 6, 7 or 8 modeled by MODELLER software.
• It mapped about 40,000 substitutions to 252 WD40 proteins from Swiss-Prot section with relatively higher confidence categories (“High”). Besides the general information of variants, we not only provided the special annotations include exact secondary structures locations, featured site identifications (hydrogen bond network, potential hotspots on the top face), but also presented the information obtained from other databases, like pathogenic predictions in dbNSFP,cancer driver mutation from the IntOgen, cancer highly recurrent mutations from the cBioportal and mutations have been experimentally shown to affect the PPIs from the IntAct.
• It deployed the updated WDSP tool with options of parameter tuning (the searching database and the iterative times), which would provide better predictions for user' own sequences.

WD40 Repeat Protein

• The WD40-repeat domains are one of the most popular interactors in protein-protein interaction (PPI) networks. By acting as scaffolds, they assemble various molecular machineries, and play versatile roles in fundamental biological processes including signal transduction, ubiquitination, cell cycle control, etc.
• WD40 domain is a β-propeller usually formed by 6-8 repeats, and the sequence of one single repeat contains 40-60 residues with conserved GH and WD dipeptides.
• Each WD40 repeat folds into a four-stranded antiparallel β-sheet (strand d, a, b and c, connected by loops), and is often stabilized by a strong side-chain hydrogen bond network which is widely and uniquely presented in WD40 proteins.
• WD40 domain has three faces, i.e. top, side and bottom faces, to mediate the interactions with partners. The top face is better studied than others, and the potential hotspot residues on this face are exposed into the solvent by the β bulge between the strand a and strand b to participate in interactions.

WDSP

• WD40 repeat protein Structure Predictor (WDSP) is developed to accurately predict the secondary structures of WD40 domains, hydrogen bond networks, and interaction hotspots.
• The WDSP tool adopts a WD40-specific position weight matrix (PWM) and PSIPRED as backends. The experimental structures used for generating the PWM have expanded from 33 to 65 and we replaced PSIPRED from V3 to V4.
• WDSP is the only one tool which can both identify the exact boundaries of WD40 repeat and their structural and functional features up to date.

Statistics

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The WDSPdb 2.0 is based on UniProtKB V201707, and the data coverage is about 10 times of WDSPdb1.0.

The statistic of all WD40 proteins in different categories

Category	WD40 Proteins	WD40 Repeats	Hydrogen Bond Network	Potential Hotspots on the Top Face	Species
Total	594,319	4,033,034	852,295	4,963,216	4,426
High	194,182	1,575,604	709,212	2,093,562	1,984
Middle	63,401	411,377	96,753	490,226	2,086
Low	336,736	2,046,053	46,330	2,379,428	4,021
Eukaryota	349,985	2,526,886	759,192	3,165,106	1,711
Bacteria	232,439	1,433,214	90,131	1,711,023	2,472
Archaea	7,272	48,997	1,779	57,419	175
Viruses	680	4,043	176	5,584	67
Homo sapiens	1,941	10,698	3,388	13,087
Mus musculus	1,398	8,955	2,674	10,943
Danio rerio	950	6,900	2,025	8,519
Oryza sativa	791	5,290	1,544	6,565
Arabidopsis thaliana	1,232	8,718	2,397	10,813
Drosophila melanogaster	688	4,682	1,282	5,718
Saccharomyces cerevisiae	176	1,197	305	1,542
Schizosaccharomyces pombe	176	1,319	377	1,685

Swiss-Prot

The statistic of Swiss-Prot section WD40 proteins in different categories

Category	WD40 Proteins	WD40 Repeats	Hydrogen Bond Network	Potential Hotspots on the Top Face	Species
Total	5,601	33,410	8,950	43,146	1,040
High	2,173	16,788	8,250	23,647	191
Middle	333	2,716	439	3,035	110
Low	3,095	13,906	261	16,464	962
Eukaryota	4,002	27,449	8,746	35,753	286
Bacteria	1,461	5,441	191	6,698	679
Archaea	46	151	1	202	26
Viruses	92	369	12	493	49
Homo sapiens	473	3,413	990	4,205
Mus musculus	436	3,160	899	3,845
Danio rerio	99	673	216	893
Oryza sativa	40	335	99	461
Arabidopsis thaliana	307	1,960	463	2,548
Drosophila melanogaster	101	699	178	912
Saccharomyces cerevisiae	176	1,197	305	1,542
Schizosaccharomyces pombe	176	1,319	377	1,685

TrEMBL

The statistic of TrEMBL section WD40 proteins in different categories

Category	WD40 Proteins	WD40 Repeats	Hydrogen Bond Network	Potential Hotspots on the Top Face	Species
Total	588,718	3,999,624	843,345	4,920,070	4,205
High	192,009	1,558,816	700,962	2,069,915	1,961
Middle	63,068	408,661	96,314	487,191	2,049
Low	333,641	2,032,147	46,069	2,362,964	3,801
Eukaryota	345,983	2,499,437	750,446	3,129,353	1,648
Bacteria	230,978	1,427,773	89,940	1,704,325	2,364
Archaea	7,226	48,846	1,778	57,217	173
Viruses	588	3,674	164	5,091	19
Homo sapiens	1,468	7,285	2,398	8,882
Mus musculus	962	5,795	1,775	7,098
Danio rerio	851	6,227	1,809	7,626
Oryza sativa	751	4,955	1,445	6,104
Arabidopsis thaliana	925	6,758	1,934	8,265
Drosophila melanogaster	587	3,983	1,104	4,806
Saccharomyces cerevisiae	0	0	0	0
Schizosaccharomyces pombe	0	0	0	0

Tutorial

Home page overview

How to batch download data?

How to use search box?

How to use WDSP predictor?

Protein detail page

Manual

Home Page

• You can hit the “Home” button at the banner to quickly jump to the home page.
• You can hit the “Predictor” button at the banner and jump to the WDSP predictor page to conduct the WD40 repeat prediction of your own sequences.
• You can use the “Help” page to learn how to use the database or predictor and understand the provided information. If you have any questions, please feel free to contact with us by “Contact” page.
• You can push the "Categories" button on the banner to access the WD40 proteins belong to the different UniProt sections, different confidence categories, taxonomy or model organisms.

• You can get started by using the search bar in the prominent of the home page to search the proteins using different classification identifier. There is a drop-down list that allows selecting the classification. You can input the gene name, UniProt accession number, UniProt entry name, entrez gene ID or organism to search.
• You can also add multiple search bars via the "Add" button on the right. Then you can search proteins by using multiple conditions.

• You can quickly learn about the WDSPdb 2.0 and the introductions of WD40 repeat proteins, WDSP tool, structural feature: hydrogen bond network, functional feature: hotspots on the top face.

• Additionally, you can get started from different classifications or pages listed below the brief introductions.

• If you use the data of WDSPdb or the WDSP in you research, please cite the associated papers.

Search Result Page

• The search results will be listed on a new page and sorted by "UniProt_AC".
• You can select specific columns and sort them according to the information of searched proteins.

Display by default	Columns	Explanation
On	Accession Number	UniProt accession number (can be sorted)
On	Section	UniProt section, Swiss-Prot ir TrEMBL (can be sorted)
On	Entry Name	The UniProt entry name (can be sorted)
On	Protein Name	Full protein name (can be sorted)
On	Organism	The Latin and English name of organism (can be sorted)
On	WDSP Category	The assigned confidence category for that protein
On	Repeat Number	The predicted WD40 repeats number (can be sorted)
Off	WDSP Score	The average repeats score of prediction

• You can export the search results list or customized selected list by multiple formats, such as .txt, .csv, .json, .xml et al ①.
• You can push the "Detail ②" button to access the detailed page of the specific WD40 protein.

Protein Detail Page

Basic protein information

• Take WDR5_HUMAN ① information page as an example.
• The WD40 proteins which are manually reviewed and corrected the secondary structures according to the PDB structures are marked by yellow pencil ②.
• The basic information of the protein is displayed by a table at the top of the page ③.
• The information items about include:

Items	Explanation
Accession Number	UniProt accession number
Gene Name	The gene symbol
Gene ID	Entrez gene ID
Protein Name	Full protein name
Organism	The Latin and English name of organism
Organism Domain	The highest taxonomic rank of organisms in the biological taxonomy
WDSP Category	The assigned confidence category for that protein
HGNC ID	The HGNC ID of the protein
Data Source	The protein is belong to the Swiss-Prot or TrEMBL
Experimental Structures of WD40 Domain	The experimental structures containing WD40 domain
Reference Sequence	protein ID or transcript ID in NCBI
Description	Alternative protein names
Functions	The annotated function in UniProt Knowledge Base
Ensembl ID	The Ensembl gene ID, transcript ID and protein ID

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The WD40 repeat and secondary structures

• In general, the WD40 repeats and secondary structures were predicted by updated WDSP. In special, they have been manually corrected according to the PDB structures when the “Reviewed reference” ① gave the PDB ID and “Average score” ② was empty.
• You can download the description of secondary structures as text format ③.
• Each line in the colored table is a single WD40 repeat. The columns described as follow table:

Column	Explanation
Repeat ID	The WD40 repeat order number
Score	The WDSP predicted score of the WD40 repeat (mannually reviewed if empty)
Start	The start site of the WD40 repeat, means the first site of the strand_d
End	The first site of the loop_cd. The end site of last repeat is the followed site of the strand_c
Strand_d	The first strand of the WD40 repeat at the side face of the structure
Loop_da	The loop connecting the strand_d and strand_a at the top-side face of the structure
Strand_a	The second strand of the WD40 repeat at the inner face of the structure
Loop_ab	The loop connecting the strand_a and strand_b at the bottom face of the structure
Strand_b	The third strand of the WD40 repeat
Loop_bc	The loop connecting the strand_b and strand_c at the top face of the structure
Strand_c	The fourth strand of the WD40 repeat
Loop_cd	The loop connecting the strand_c and strand_d of next WD40 repeat at the side-bottom face of the structure
H_bonds	The residues participate in forming hydrogen bond networks of WD40 repeat (blue residues)
Hotspots	The potential hotspost residues on the top face (red residues)

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Structure model & Variants (if mapped)

• All of the 3D structure models we displayed were modeled. And only the proteins which repeat number among 6, 7, 8 have models.
• When the template is the PDB ID, the structure used that experimental structures as template ①.
• When the template is the UniProt Accession Number, the structure used that protein model as the template.
• The secondary structures of 3D structure models have been annotated by predicted secondary structures. In the default color scheme, the yellow indicated the β-strand, the magenta indicated the α helix and the white indicated the loops ②.
• You can push the buttons on the action bar to view featured sites, download the 3D structure models or associated sequences, and change the structural display style ③.
• Additionally, you can check the specific variants in the checkbox table at the right side to display ④.
• The display color: sites of variants is grey; sites of hydrogen bond networks is blue; sites of variants on hydrogen bond networks is cyan; sites of potential hotspots is red; sites of variants on hotspots is pink;
• ⑤ The secondary structure locations of the variants in the WD40 repeats. For example: "Sa_6" means the sixth residue of strand a; "Lda_7" means the seventh residue of loop da.

Button	Explanation
Template	Jump to the template page
	View the featured sites include potential hotspots on the top face and hydrogen bond networks
	Download the 3D structure models or associated sequences
	Change the structural display style: style, color schemes or background
	Reset all actions
	Expand to full screen to view
	Let the structure spin
	Jump to the help of 3D structure viewer

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The variants table

• The table showed the human missense variants of WD40 proteins which belong to “High” confidence category.
• These mutations/variants were collected from different datasets, include 1000 Genomes, Clinvar, ExAC, Cosmic.
• You can select and present specific columns about the mutations/variants information and sort them in the dynamic table.

Display by default	Column	Explanation
On	Site	Variant site corresponding to the UniProt sequence
On	Substitution	The single amino acid substitution of the variant
On	2D Location	The secondary structure location of the variant in that WD40 repeat
On	Repeat ID	The ordinal number of WD40 repeat where the variant are located
On	Featured site	The wild type residue of the variant is the member of the hydrogen bond network or hotspots on the top face
On	Resource	The data source or database of the variant
On	Clinical Info	The clinical information of the variant from ClinVar or Cosmic. Please see.
On	Cancer Driver	The associated cancer types driven by that variant, as annotated in IntOGen.Please see.
On	Highly Recurrent	Whether the variant is highly recurrent in cancer, as annotated in cBioPortal. Please see the answer of "Which resources are integrated for variant annotation?" at the FAQ page of cBioPortal.
On	PPI Effect	The variant effect on the interaction and specific partner, as annotated in the IntAct. Please see.
Off	Reference CDS Changes	The transcript codon changes of the variant
Off	Reference	The PMID of the reference which reported the variant
Off	Allele Frequency	The allele frequency of the variant from the dataset
Off	Chromosome Coordinate	The codon change site in the chromosome of the variant
Off	SIFT_score	Sorting Intolerant From Tolerant score, range from 0 to 1
Off	SIFT_pred	Prediction of SIFT scores: "T(olerated)" or "D(amaging)", The score cutoff between "D" and "T" is 0.05.
Off	MutationAssessor_score	MutationAssessor functional impact combined score, The score ranges from -5.135 to 6.49 in dbNSFP.
Off	MutationAssessor_pred	MutationAssessor's functional impact of a variant : predicted functional, i.e. high ("H") or medium ("M"), or predicted non-functional, i.e. low ("L") or neutral ("N"). The MAori score cutoffs between "H" and "M", "M" and "L", and "L" and "N", are 3.5, 1.935 and 0.8, respectively.
Off	FATHMM_score	FATHMM default score (weighted for human inherited-disease mutations with Disease Ontology) (FATHMMori). Scores range from -16.13 to 10.64. The smaller the score the more likely the SNP has damaging effect.
Off	FATHMM_pred	If a FATHMM score is <=-1.5 (or rankscore >=0.81332) the corresponding nsSNV is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)".
Off	MetaSVM_score	Support vector machine (SVM) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from -2 to 3 in dbNSFP.
Off	MetaSVM_pred	Prediction of our SVM based ensemble prediction score,"T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.
Off	MetaLR_score	Logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1.
Off	MetaLR_pred	Prediction of our MetaLR based ensemble prediction score,"T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5.
Off	CADD_phred	CADD score.The larger the score the more likely the SNP has damaging effect.If you would like to apply a cutoff on deleteriousness, e.g. to identify potentially pathogenic variants, we would suggest to put a cutoff somewhere between 10 and 20. Maybe at 15, as this also happens to be the median value for all possible canonical splice site changes and non-synonymous variants. However, there is not a natural choice here -- it is always arbitrary. We therefore recommend integrating C-scores with other evidence and to rank your candidates for follow up rather than hard filtering.
Off	ExAC_AC	Allele count in total ExAC samples (60,706 samples)
Off	ExAC_AF	Allele frequency in total ExAC samples
Off	ExAC_pLI	"The probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 data
Off	ExAC_pRec	"The probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 data
Off	GDI	Gene damage index score, "a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population" from doi: 10.1073/pnas.1518646112. The higher the score the less likely the gene is to be responsible for monogenic diseases.
Off	Essential_gene	Essential ("E") or Non-essential phenotype-changing ("N") based on Mouse Genome Informatics database. from doi:10.1371/journal.pgen.1003484
Off	Polyphen2_HDIV_score	Polyphen2 score based on HumDiv. The score ranges from 0 to 1
Off	Polyphen2_HDIV_pred	Polyphen2 prediction based on HumDiv, "D" ("probably damaging", HDIV score in [0.957,1]), "P" ("possibly damaging", HDIV score in [0.453,0.956]) and "B" ("benign", HDIV score in [0,0.452] ). Score cutoff for binary classification is 0.5 for HDIV score
Off	Polyphen2_HVAR_score	Polyphen2 score based on HumVar. The score ranges from 0 to 1.
Off	Polyphen2_HVAR_pred	Polyphen2 prediction based on HumVar, "D" ("probably damaging", HVAR score in [0.909,1]), "P" ("possibly damaging", HVAR in [0.447,0.908]) and "B" ("benign", HVAR score in [0,0.446]). Score cutoff for binary classification is 0.5 for HVAR score

Clinical Information

ClinVar:

ClinVar uses official terminology for clinical information. The authorities clinical information are detailed on their Nomenclature page.

Cosmic:

Format of clinical information:
Primary Tissue|Tissue Subtype1|Tissue Subtype2|Tissue Subtype3:Histology|Histology Subtype 1|Histology Subtype 2|Histology Subtype 3

Interpretation

Primary Tissue	The primary tissue from which the sample originated. More details on the tissue classification can be found here
Tissue Subtype 1	Further sub classifications of the samples tissue of origin
Tissue Subtype 2	Further sub classifications of the samples tissue of origin.
Tissue Subtype 3	Further sub classifications of the samples tissue of origin.
Histology	The histological classification of the sample
Histology Subtype 1	Further histological classifications of the sample
Histology Subtype 2	Further histological classifications of the sample
Histology Subtype 3	Further histological classifications of the sample
NS	Not specify

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Cancer Driver

The abbreviation of cancer types:

Abbreviation	Full Name
ALL	acute lymphoid leukemia
AML	acute myeloid leukemia
BLCA	bladder carcinoma
BRCA	breast carcinoma
CLL	chronic lymphocytic leukemia
CM	cutaneous melanoma
COREAD	colorectal adenocarcinoma
DLBC	diffuse large B cell lymphoma
ESCA	esophageal carcinoma
GBM	glioblastoma multiforme
HC	hepatic carcinoma
HNSC	head and neck squamous cell carcinoma
LGG	lower grade glioma
LUAD	lung adenocarcinoma
LUSC	lung squamous cell carcinoma
MB	medulloblastoma
MM	multiple myeloma
NB	neuroblastoma
NSCLC	non small cell lung carcinoma
OV	serous ovarian adenocarcinoma
PA	pilocytic astrocytoma
PAAD	pancreas adenocarcinoma
PRAD	prostate adenocarcinoma
RCCC	renal clear cell carcinoma
SCLC	small cell lung carcinoma
STAD	stomach adenocarcinoma
THCA	thyroid carcinoma
UCEC	uterine corpus endometrioid carcinoma

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PPI Effect

Format of PPI effect:

Effect type:Interaction partner

There are several effect types of mutations covered, the terms used have been described in the PSI-MI controlled vocabularies, accessible at www.ebi.ac.uk/ols/ontologies/mi:

• Mutation (MI:0118): A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event. This root term is used when there is a mutation present in a protein and the wild type version has not been tested or shown to interact in the referenced paper.
  • Mutation causing an interaction (MI:2227): A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact.
  • Mutation decreasing interaction (MI:0119): Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
    • Mutation decreasing interaction rate (MI:1130): Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
    • Mutation decreasing interaction strength (MI:1133): Region of a molecule whose mutation or deletion decreases significantly interaction strength.
    • Mutation disrupting interaction (MI:0573): Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
      • Mutation disrupting interaction rate (MI:1129): Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction).
      • Mutation disrupting interaction strength (MI:1128): Region of a molecule whose mutation or deletion totally disrupts an interaction strength.
      
  • Mutation increasing interaction (MI:0382): Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
    • Mutation increasing interaction rate (MI:1131): Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
    • Mutation increasing interaction strength (MI:1132): Region of a molecule whose mutation or deletion increases significantly interaction strength.
  • Mutation with no effect (MI:2226): A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type.

Predictor Help

• You should input a jobname to name your submitted task. This is not allowed by empty ①.
• You should input your email address ② to get your prediction result link even you won’t leave the page. The resulting link will be saved for you for a month.
• You can select the iterative times ③ to get better results. The presented result just present the best one in all of your predictions.
• There are two BLAST searching databases ④: Swiss-Prot or UniRef90. You could choose the much larger database, UniRef90, to get better predictions. But you should notice chose the UniRef90 would be very time consuming.
• The input sequences must be standard FASTA format.
• The maximum input up to 5 sequences and any one length could not be less than 40. You can hit the “EXAMPLE” ⑤ to get the example input.
• Please try to cut the known non-WD40 regions from your sequence, thus the prediction would become faster.
• Push the “SUBMIT” button ⑥ to submit your task and it would jump to the result page when the task finished. In addition, your email would receive the result link at the same time.

Citations

If you use the data of WDSPdb or the WDSP predictor in you research, please cite the following papers:

1. Ma, J., An, K., Zhou, J.B., Wu, N.S., Wang, Y., Ye, Z.Q., Wu, Y.D. (2019). WDSPdb: an updated resource for WD40 proteins. Bioinformatics, [PMID: 31161214]
2. Wang, Y., Hu, X.J., Zou, X.D., Wu, X.H., Ye, Z.Q. and Wu, Y.D. (2015) WDSPdb: a database for WD40-repeat proteins. Nucleic Acids Res, 43 , D339-344. [PMID: 25348404]
3. Wang, Y., Jiang, F., Zhuo, Z., Wu, X.H., Wu, Y.D. (2013). A Method for WD40 Repeat Detection and Secondary Structure Prediction. PLoS ONE , 8(6) , e65705. [PMID: 23776530]
4. Wu, X.H., Wang, Y., Zhuo, Z.,Jiang, F., Wu, Y.D. (2012). Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by beta-bulges and DHSW tetrads. PLoS ONE , 7(8) , e43005. [PMID: 22916195]

Frequently Asked Questions