Searching ProNIT

Terms Explanation
ProNIT Entry Definition:ProNIT entry number. Each entry in ProNIT is identified with a unique numerical number, starting from 1. Please see the ProNIT Entry list for more details.
Query format: Enter the entry number of the data that has to be retrieved.
Query example : To retrieve the data for the entry number 100, enter the query as . To retrieve the data between the entry numbers 100 and 200 (including 100 and 200), enter the query as .
Protein Name Definition: Name of the protein. Please see the Protein list available in our database.
Query format: Enter the protein name that has to be queried. Search strings are case insensitive. Words sperated by spaces are considered as single word by the query.
Query example : To retrieve the data for the "cAMP protein", enter the query as .
Protein Source Definition: Source of the protein. Please see the Protein Source list available in our database.
Query format: Enter the protein source that has to be queried. Search strings are case insensitive. Words sperated by spaces are considered as single word by the query.
Query example : To retrieve the data for the source "Escherichia coli", enter the query as .
PDB_Code Definition: Protein Data Bank entry code for the protein (PDB_FREE) or protein-nucleic acid complex (PDB_COMPLEX). Please see the PDB code list available in our database.
Query format: Enter the four letter PDB-Code that has to be queried. Search strings are case insensitive.
Query example : or . This will fetch all the data from the database where this PDB code is present. Protein chain information is not available. Format like is not acceptable.
Protein Sequence Definition: Sequence of the protein fragment used in the study.
Query format: Enter the single letter amino acid code that has to be queried. Search strings are case insensitive.
Query example : In order to query for a protein sequence "AAAD", enter the query as or .
Mutation Definition: Mutation of the protein. Single: single mutation, Double: double mutation, Multiple: multiple mutation, Wild: no mutation (Wild protein).
Query format: Enter amino acid single letter code.
Query example : In order to fetch all the mutations of K with M at any position, enter the query as To . Multiple boxes can be checked to search for Single, Double, Multiple mutations and Wild proteins. In the case of insertion or deletion mutations, all inserted/deleted residues appear along with the preceding residue that corresponds to the residue number at which the mutation occurs (for example, A 378 AVL refers that the two amino acid residues "V" and "L" are inserted at 378th position where the residue "A" is present in the wild type. It is represented conversely for the deletion, viz, AVL 378 A, indicating that the amino acids "V" at 379 and "L" at 380 are deleted). In order to retrive an entry with the mutation A to AVL at any position, enter the query as To
Sec_Str Definition: Secondary Structural Information of the residue at mutant site (Helix, Strand, Turn and Coil) taken from PDB database.
Query format: Check the appropriate boxes to get the data with Helix/Sheet/Turn/Coil secondary structure at the mutant site. Multiple boxes can be checked.
Query example : In order to query the data with helix secondary structure, enter the query as
Helix Sheet Turn Coil
ASA_Free Definition: Accessible surface area (ASA) of the residue (contribution from the side chain) in wild type, computed using the program GETAREA 1.1 ( http://www.scsb.utmb.edu/cgi-bin/get_a_form.tcl), expressed in units of A2. Accessibility (%) is defined as the ASA of the residue (X) in its parent protein, computed with GETAREA, to "random coil" value per residue.
Query format: Enter the range of ASA value that has to be queried.
Query example : In order to query the ASA values within the range 20 and 60 (including 20 and 60), enter the query as
To and select % or A^2.
Nucleic Acid Name Definition:Name of the nucleic acid.
Query format: Enter the name of the nucleic acid to be queried. Search strings are case insensitive.
Query example : To retrieve the data for the "cDNA", enter the query as .
Nucleic Acid Source Definition: Source of the nucleic acid.
Query format: Enter the source of the nucleic acid to be queried. Search strings are case insensitive.
Query example : To retrieve the data for the "Synthetic nucleic acid", enter the query as .
Nucleic Acid Type Definition:Nucleic Acid Type: ssDNA (single stranded DNA), dsDNA (double stranded DNA) or RNA.
Query format: Check the type of the nucleic acid. By default the search selects all types
Query example : In order to query the data for RNA , enter the query as
dsDNA ssDNA RNA
NDB_Code Definition:Nucleic Acid Database entry code for the protein-nucleic acid complex. Please see the NDB code list available in our database.
Query format: Enter the NDB_Code that has to be queried. Search strings are case insensitive.
Query example : or . This will fetch all the data from the database where this NDB code is present.
Nucleic Acid Sequence Definition:Sequence of the nucleic acid (5' to 3').
Query format: Enter the sequence of the nucleic acid to be queried. Search strings are case insensitive.
Query example : In order to query for a nucleic acid sequence "AATTGG", enter the query as or .
Method Definition:Experimental method used for studying the Protein-nucleic acid binding (e.g. Isothermal Titration Calorimetry (ITC), Differential Scanning Calorimetry (DSC), Fluorescence , Footprinting, Gel shifts, Filter Binding, etc. ).
Query format: Select the option from the list. Only one option can be selected at one time.
T Definition: The temperature (degree celsius) at which the measurements were performed.
Query format: The query retrieves the T values for the wild proteins by deafult. If the mutation field is selected for mutant proteins, the query retrieves the T values for the mutant proteins.
Query example : To retrieve data for T values between 25 and 35 (including 25 and 35), enter the query as
To   ° C
pH Definition: The pH value at which the measurements were made.
Query format: The query retrieves the pH values for the wild proteins by deafult. If the mutation field is selected for mutant proteins, the query retrieves the pH values for the mutant proteins.
Query example : To retrieve data for pH values between 4 and 7 (including 4 and 7), enter the query as To
Kd Definition: Dissociation constant for protein-nucleic acid binding in molar [M].
Query format: The query retrieves the Kd values for the wild proteins by deafult. If the mutation field is selected for mutant proteins, the query retrieves the Kd values for the mutant proteins.
Query example : To retrieve data for Kd values between 2 x 10 -10 and 5 x 10 -6 M, enter the query as
x 10    To   x 10 M
dG Definition:Free energy change for protein-nucleic acid binding [kcal/mol].
Query format: The query retrieves the dG values for the wild proteins by deafult. If the mutation field is selected for mutant proteins, the query retrieves the dG values for the mutant proteins.
Query example : To retrieve data for dG values between -1 and 2 kcal/mol(including -1 and 2), enter the query as
To kcal/mol
dH Definition:Enthalpy change for the Protein-nucleic acid binding [kcal/mol].
Query format: The query retrieves the dH values for the wild proteins by deafult. If the mutation field is selected for mutant proteins, the query retrieves the dH values for the mutant proteins.
Query example : To retrieve data for dH values between -1 and 2 kcal/mol (including -1 and 2), enter the query as
To kcal/mol
dCp Definition:Heat capacity change for the Protein-nucleic acid binding [kcal/mol/K].
Query format: The query retrieves the dCp values for the wild proteins by deafult. If the mutation field is selected for mutant proteins, the query retrieves the dCp values for the mutant proteins.
Query example : To retrieve data for dCp values between -1 and 2 kcal/mol/K (including -1 and 2), enter the query as To kcal/mol/K
Author Definition: Names of the authors. Please see the Author list available in our database.
Query format: Enter the name of the author or names of the authors to retrieve the data. Search strings are case insensitive.
Query example : To retrieve the data by the author "Oda M", enter the query as and to retrieve the data by the authors "Oda M" and "Nakamura H", enter the query as
Year Definition:Year of the publication of the reference paper from which the data has been taken. Please see the Reference list available in our database.
Query format: Enter a particular year or years to retrieve the data for this period.
Query example : To retrieve the data for the year 2000, enter the query as To and to retrieve the data between the years 2000 and 2004 (including 2000 and 2004), enter the query as To
Keywords Definition:List of keywords.
Query format: Enter the search keyword. Select the boolean operator AND or OR for multiple keyword search. Search strings are case insensitive.
Query example : To get all the data for the keyword "c-Myb", enter the query as . To retrieve all the data for a combination of search keywords "c-Myb" and "binding", enter the query as .To retrieve all the data for a combination of search keywords "specific" or "binding", enter the query as .
Display Options Definition:The field display option for the query result page.
Query format: Check the fields that has to be displayed in the query result page.
Sorting Options Definition:The sorting order priority.
Query format: Select the sorting order priority from the list. In the list, aa_before_mut: amino acid before mutation, aa_after_mut: amino acid after mutation and aa_position: mutation position.
Query example : To sort the data with the sorting order Kd_Wild, T, pH and Year, enter the query as
Entries per page Definition:Number of entries displayed in one page.
Query format: Enter a numerical number. The default is 50 entries per page.
Query example : To display 100 entries per page, enter the query as
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Input Format of Searching Items

Terms Type Input Format
Protein Name
Protein Source
Method
Keywords
Author		 Text Multiple words can be entered with spaces. But the query will take it as a single word.
Two wild cards can also be used: (1) * for a string of characters; (2) ? for a single character. If * and ? were to be used as real characters, place "\" (backslash) before them.
For Keywords and Author fields these can be combined with AND and OR logical operations to form more complex patterns.
Protein Sequence
Nucleic Acid Sequence		 Sequence Pattern of sequence.
Use single letter code.
( ) -- repetition of pattern within ( )
(S,T)2 = S or T repeated twice
(GM,P)x4(Y,C) = GM or P followed by Y or C after 4 any amino acids
{ } -- number of repetitions of a preceding amino acid or pattern within ( )
PAST{n,} = PAS followed by T repeated n~(n+50) times
PAST{} = PAS followed by T repeated 0~50 times
PA(ST){,n} = PA followed by ST repeated 0~n times (n<50)
P(QR,S,T){n,m} = P followed by QR or S or T repeated n~m times
~ -- not matching
PA~(S,T) = PA followed by any amino acids except S or T
< -- the following pattern occurs at the beginning of the range being searched
&ltPAST = P must be at the beginning of the sequence range
> -- the preceding pattern occurs at the end of the range being searched
PAST> = T must be at the end of the sequence range