dbMPIKT Document
dbMPIKT is a free database that can browse the data and detailed information in the web, download the data file. It includes home page, Browse, Document, Upload, Download and Contact us. The dbMPIKT requires a modern web browser with JavaScript enabled. The following browsers have been throughly tested with dbMPIKT: You can enter the database home page via Internet Explorer version 8.0, Mozilla Firefox version 54.0.1 or Chrome version 59.0.
Data description
Kinetic data: Kd (dissociation rate constant); Kon (association rate); Koff (dissociation rate)
Thermodynamic data: ΔG (change in binding free energy); ΔΔG (difference in binding free energy change between mutant and wild-type complex);                                     ΔH (change in enthalpy); ΔS (change in entropy).
Data analysis
Mutation number
For the number of mutations, we performed simple statistics based on different sources. The statistical results are as follows:
Table 1 The statistics of mutation number for the four data sets.
Data sets SKEMPI data BID data AB-Bind data Curated data Total
Mutation number 3046 256 815 1174 5291
Mutation type
For mutation type, we can explain from two aspects. First, the number of mutations can be divided into single mutations, double mutations, and multiple mutations. Detailed data analysis is shown in Table 2 and Figure 1.
Table 2 The statistics of mutation type for the four data sets.
Data Single mutant Double mutant Multiple mutant Total
alanine other alanine other alanine other
SKEMPI 1057 1259 211 153 62 304 3046
BID 256 0 256
AB-Bind 267 173 28 175 2 170 815
Curated data 673 338 49 88 15 12 1174
Total 2453 1770 288 416 79 486 5291
Figure 1 The data distribution of the four data sets.
As shown above, it is clear that the single mutation data in our data is the most. Second, we can analyze the mutated amino acid species. In order to highlight the single mutation data, we analyzed the number of mutations for each type of amino acids in the single mutation data and the results are shown below. It is worth mentioning that the number of amino acids in a single mutation is the most.
Table 3 Kinds and the number of single mutant amino acids statistics
Amino acid/Data Sources SKEMPI BID AB-Bind Curated data Total
Hydrophobic A 1057 256 267 673 2253
I 53 0 2 11 66
L 77 3 17 97
M 60 3 12 75
V 74 12 12 98
W 54 14 13 81
Y 56 14 14 84
F 94 8 23 125
Polar S 71 11 21 103
T 48 6 9 63
N 60 15 21 96
Q 78 25 21 124
Positive R 76 15 18 109
K 98 7 29 134
H 54 2 10 66
Negative D 76 15 27 118
E 83 12 35 130
Other C 45 1 14 60
G 59 7 21 87
P 43 1 9 53
Total 2316 256 440 1010 4022
Figure 2 Kinds and the number of single mutant amino acids statistics for four sets.
Protein pair source
In our database, all the mutation data comes from four datasets, so we analyze the source of protein pairs is also divided into four parts, the curated data is divided into two parts: one is from NCBI, another is derived from PDB.
Table 4 The statistics of protein-protein complexes for the four data sets.
Data sets SKEMPI data BID data AB-Bind data Curated data Total
PDB NCBI
protein-protein complexes 159 42 27 60 41 254
It is worth noting that there will be duplicates of protein complexes between different data sets. In total, we have 254 protein-protein complexes. If you want to get all the protein pairs, click here.
Among them, we analyzed the source of protein pair. The proteins are human proteins, mus musculus proteins, bos taurus proteins and so on. Among them, human proteins are the most type of proteins.
Figure 3 Protein pair source for all protein-protein complexes.
Network map construction
For all pairs of protein interactions, we used the cytoscape tool to construct a network map, as shown in Figure 3, showing Part of the interaction. If you want to get a map of all protein interactions, click here.
Figure 4 Part of the interaction on the network map.
Each node in the picture represents a protein, and the connection between nodes represents an interaction. If you want to build a network map, download the cytoscape tool from the Download interface.
一  Home
Please visit the home page of dbMPIKT in your browser.
You can learn about brief introduction and statistics of dbMPIKT. Click here to download the detailed information about data and click the image on the right to link to the relevant website. In addition, you can select the data list in the quick search and this mutation information search retrieves lists of mutants based on PDB ID.
二  Browse
In the browse page, you can see all mutations in dbMPIKT, you also can choose the data you want to browse based on different sources( SKEMPI, AB-Bind, BID and dbMPIKT data )
In this page, you will find all information about mutants, such as PDB ID, mutation, PubMed ID and so on. The four datasets are displayed in detailed page. Click on the PDB ID or PubMed ID can be link to the corresponding website to get more detailed information. In addition, on the Browse, we created a new table to place the user's new upload data.
三  Download
In this page, you can freely download all data based on different sources.
四  Upload
In this upload page, users can submit information about mutations, we will add this information in dbMPIKT. Among them, the asterisk is marked as required.
五  Contact us
If you have any question or revise wrong information in dbMPIKT. Please send us email directly. Click the image on the right to link to the relevant website.