In the field of “Please enter your keyword and search for SBP”, users can find Synthetic Binding Protein (SBP) entries by searching SBP name or synonym, protein scaffold name and target name among the entire textual component of SYNBIP. If you want Protein Scaffold (PSS) entries or Binding Target (BTS) entries, you can also search scaffold name, SBP name or target name and select the corresponding button below the textual component.

Query can be submitted by entering keywords into the main searching frame. Users can specify part or full name in the text field. To facilitate a more customized input query, the wildcard characters of “*”, “-” and “?” are also supported in SYNBIP.

(1) If search “Monobody BMS-962476” and click the “Synthetic Binding Protein (SBP)” button, find two entries with SBP name “Monobody BMS-962476” and “Monobody BMS-986192”. If you want only entry with SBP name “Monobody BMS-962476”, double quotation marks are required when you search the SBP name;

(2) If search “Monobody” and click the “Protein Scaffold (PSS)” button, find only entry with PSS name “Monobody”;

(3) If search “EGFR” and click the “Binding Target (BTS)” button, find related entries with BTS name “Epidermal growth factor receptor” or “EGFR”;

(4) If search “Green fluorescent protein”, a target name and click the “Synthetic Binding Protein (SBP)” button, find entries with the SBP names including “Affitin anti-GFP D8”, “alphaRep protein anti-GFP clone A”, and so on, all of which bind to the target “Green fluorescent protein”;

(5) If search “BMS-962476” and click the SBP button, four entries “Monobody BMS-962476”, “Monobody BMS-986192”, “Monobody Pegdinetanib” and “Monobody Talditercept alfa” will be find. Synonyms of the latter two SBPs contain “BMS”. Here “-” is equal to the word “or”;

(6) If search “Fynomer anti-Chymase 4C-?4” and click the SBP button, find entries with SBP names like “Fynomer anti-Chymase 4C-A4” and “Fynomer anti-Chymase 4C-E4”. Here “?” represents any single English letter and is only effective in a phrase consisting of two or more words;

(7) If search “BMS*” and click the SBP button, find all SBPs whose SBP name or synonyms have this word “BMS”. Here “*” represents an arbitrary string.

In the field of "Search for PSS", users can find PSS entries by selecting PSS name, SBP name and parental protein name.

1. Search for PSS by PSS Name

In this field of "Search for PSS by PSS Name", users can select one of protein scaffolds and get the PSS information.

For example: if search “Affibody”, users can access to basic information of the PSS. If you want to know more about this PSS, you can click the corresponding "PSS Info" button.

2. Search for PSS by SBP Name

In this field of "Search for PSS by SBP Name", users can select one of SBPs and get corresponding PSS information of this SBP.

For example: if select “Monobody BMS-962476”, users can access to corresponding PSS entry of the SBP. If you want to know more about this PSS, you can click the corresponding "PSS Info" button.

3. Search for PSS by Parental Protein Name

In this field of "Search for PSS by Parental Protein Name", users can select one of parental proteins and get corresponding PSS information.

For example: if select "10th domain of Fibronectin III", users can access to corresponding PSS entry of the parental protein. If you want to know more about this PSS, you can click the corresponding "PSS Info" button.

In the field of "Search for Binding Target of SBP (BTS)", users can find BTS entries by selecting BTS name, BTS family name and SBP name.

1. Search for BTS by BTS Name

In this field of “Search for BTS by BTS Name”, users can select one of binding targets and get the BTS information.

For example: if search “Epidermal growth factor receptor”, users can access to basic information of the BTS from different organisms. If you want to know more about the BTS, you can click the corresponding “BTS Info” button.

2. Search for BTS by BTS Family Name

In this field of “Search for BTS by BTS Family Name”, users can select one of BTS families and get corresponding BTS information of the target family.

For example: If select “Tumor necrosis factor family”, users can access to corresponding BTS entries of the family. If you want to know more about a BTS, you can click the corresponding "BTS Info" button.

3. Search for BTS by SBP Name

In this field of "Search for BTS by SBP Name", users can select one of SBPs and get corresponding BTS information.

For example: if select “Monobody BMS-962476”, users can access to corresponding BTS entries of the SBP. If you want to know more about this BTS, you can click the corresponding “BTS Info” button.

4. BTS information

By clicking the “BTS Info” button, the detailed information page of “Epidermal growth factor receptor” will be displayed. Details of BTS are divided into two parts, “General Information of BTS” and “Synthetic Binding Protein (SBP) Targeting This BTS”. The general information of “Epidermal growth factor receptor” includes its “BTS Name”, “Synonyms”, “BTS Type”, “Family”, “Gene Name”, “Organism”, “Function”, “UniProt ID”, “UniProt Entry”, “PFam”, “Gene ID”, “Sequence” and “Sequence Length”. If you want to know more about this target, you can link to other related databases by clicking the corresponding IDs.

“Synthetic Binding Protein (SBP) Targeting This BTS” includes all of SBPs binding to this target. Here, a statistical table is displayed. Users can get information of “SBP Name”, “Highest Status of SBP”, “Mechanism of SBP to the target”, “Affinity between SBP and the target” and “Application of SBP”. If you want to know more about a SBP, you can click the “SBP Info” button.

Besides traditional keywords search, we also supply SBP target sequence similarity query for searching similar sequences against all SBP targets with available sequence information in SYNBIP. The similarity degree of those identified SBP targets will be evaluated by BLAST program, and with the sequence identities listed out. Using “Human GTPase HRas” as an example, 2 target sequences will be identified with identities of 87% and 100% (itself), respectively. Links to the detail information of identified targets are also provided. By using the found targets of interested, users can select suitable SBPs for protein function and function study.