hydrocluster 0.2.0

Cluster analysis of hydrophobic or charged regions of macromolecules. The program is based on the DBSCAN algorithm.

Hydrocluster - Bioimformatics Tool

Short description

The program Hydrocluster is designed to determine the position, size and content of hydrophobic, hydrophilic and charged clusters in protein molecules. The program is based on the DBSCAN algorithm.

Keywords: molecular modeling, bioinformatic, protein structure, hydrophobic core, hydrophobic cluster, DBSCAN

Installation

pip install --upgrade hydrocluster

(or pip3 in distributive with default python 2 version)

User Interface

Command line

The program is called with the command ’hydrocluster’ and following parameters:

hydrocluster [-h][-i INPUT][-emin EMIN][-emax EMAX][-es ESTEP]
[-smin SMIN][-smax SMAX][-g {tkgui,cli,testlist}][-o OUTPUT][-c CHAINS]
[-rl RESLIST][-pt{hydropathy,menv,fuzzyoildrop,nanodroplet,aliphatic_core,hydrophilic,positive,negative}]
[-pH PH][-sc {si_score,calinski,dbcv}][-nf][-na][-eps EPS][-min_samples MIN_SAMPLES]

Arguments:

-h, --help
show help message and exit

-i INPUT, --input INPUT
Input file name (pdb,cif, ent, .hjson) - pdb file name, cif file name, individual id pdb or hjson configuration file name for testlist

-emin EMIN, --emin EMIN
Minimum EPS value (Å). Default=3.0

-emax EMAX, --emax EMAX
Maximum EPS value (Å). Default=15.0

-es ESTEP, --estep ESTEP
Step of EPS (Å). Default=0.1

-smin SMIN, --smin SMIN
Minimum MIN SAMPLES. Default=3

-smax SMAX, --smax SMAX
Maximum MIN SAMPLES. Default=50

-g {tkgui,cli,testlist}, --gui
UI modes. Default=’tkgui’ (tkgui - graphic interface, cli - command line, testlist - using testlist module for data processing (see -i filename.txt and -o filename of data base).

-o OUTPUT, --output OUTPUT
Output directory name/file name or db name

-c CHAINS, --chains CHAINS
Selected chains. Default=None

-rl RESLIST, --reslist RESLIST
Selected amino acid residues. Default=None

-pt{hydropathy,menv,fuzzyoildrop,nanodroplet,aliphatic_core,hydrophilic,positive,negative}, --ptable
Property table for weighting. Default=’hydropathy’

-pH PH
pH value for calculatation of partial charges (positive or negative). Default=7.0

-sc {si_score,calinski,dbcv}, --score {si_score,calinski,dbcv}
Score coefficient. Default=’calinski’

-nf, --noise_filter
Activate filter of noise for scoring function (Not recommended!!!).

-na, --noauto
No automatic mode.

-eps EPS
EPS value (Å). Default=3.0

-min_samples MIN_SAMPLES
MIN SAMPLES value. Default=3

At startup of hydrocluster without any parameters the program opens with graphics interface.

Examples:

hydrocluster -i 1atg.pdb -g cli -o 1atg

Processing of file_name.pdb by command line interface and file_name folder on return

File_name folder consists of file_name.py file for processing by pymol, binary file (.dat) with saved session state, file_name.log file with saved log-data and two png files with pictures.

hydrocluster -g testlist -i defaultt.hjson

Reading of configuration file default.json and processing it by testlis. An example of a configuration file (with parameter comments) can be found at https://github.com/alashkov83/hydrocluster/blob/master/PDB_LISTS/default.hjson. Project_name.db file and project_name_data folder consisting of tree structure with data files will be returned.

Graphical User Interface

GUI was realized using Tkinter. It consists of a panel for selecting the operation mode, a window for graphical representation of clustering results Cluster analysis, and a window for displaying log file.

At the beginning of working with the graphical interface, it is necessary to select the desired hydrophobicity/hydrophilicity table in the sub-window of the mode selection window, select the method for scoring of clustering in the metrics window and run on Manual (Manual mode -> Start) or automatic mode of operation (Auto mode -> Start) in one of the underlying windows. In the automatic mode, the optimal parameters eps and min_samples are selected by enumeration within the given boundaries and with the given step. Upon completion of the work in the automatic mode, when you click Options -> Solution analysis -> Autotune colormap, you can get a graphical interpretation of the process of selecting the optimal values namely dependencies min_samples (eps) and min_samples (eps³). The point corresponding to the optimal parameters is marked in color.

The Cluster analysis window presents a three-dimensional image of clusters selected by the program in a protein molecule. Appropriate mtnu sections allow you to make a coordinate grid in the image and get a brief comment on the picture.

The Log window shows the numerical results of clustering, namely the number of chains and clusters, the percentage of noise and the optimal values of the hyperparameters (eps,min_samples) and the metric used. Further study of the macromolecule can be carried out using the PyMol program (Options-> OpenPyMol).

Menu options:

File->

Open File - opens PDB or mmCIF file on a disk
Open ID PDB - opens file from RSCB PDB data bank with ID PDB
Load State - loads program state, saved in file
Save PyMOL script - saves script (.py) for further processing with PyMOL
Save State - saves the current state of program in file
Save Picture - saves the clustering result in png format file
Save LOG - saves log file of the current session
Quit - quit from the program

Options->
Select clustering solution -> By local max (min) - shows other solutions of cluster analysis by local extrema of scoring for make choice its
Select clustering solution -> By max (min) values - shows other solutions of cluster analysis by values of scoring for make choice its
Solution analysis -> Autotune colormap - shows graphs obtained as a result of clustering parameters selection. Marked point corresponds optimal values of eps and min_samples
Solution analysis -> Autotune 3D-map - shows 3D-graph obtained as a result of clustering parameters selection
Solution analysis -> Scan by parameter - scans some values of clustering solutions by one of the parameter (eps or min_samples) when second parameter are fixed
Open PyMol - opens PyMol for further data display
About Protein - displays information about protein
Plot settings -> Plot grid - makes coordinate grid in the Cluster analysis window
Plot settings -> Plot legend - displays the brief description of the picture
Dmod (experimental, checkbox) - modification interpoint distances, instead clusterization points weights. moddist(u, w) = dist(u, w)/(w u)/2)), where w and u - weighting coefficients of points
Clear log - clears log information in the appropriate window

Help->
About - displays information about program, its license and version, and version of scikit-learn installed on the computer
Readme - opens system web-browser and shows this paper

Theory

Hydrophobic cores and hydrophobic clusters play an important role in the folding of the protein, being the skeleton for functionally important amino acid residues of enzyme proteins. In the cases of ligands of amphiphilic nature, the hydrophobic clusters themselves are included in the functionally important regions of the molecules. The interaction with them should be taken into account, for example, when evaluating molecular docking solutions. Hydrocluster programm is based on ensity-Based Spatial Clustering of Applications with Noise (DBSCAN) [1]. Atomic coordinates, their type and description of amino acid residues (a. r.) and chemical groups [2] are loaded from a file of the PDB, mmCIF formats, or directly from the Protein Data Bank. For each a.r. (or chemical group) from the table of relative hydrophobicity center of mass of non-H atoms is calculated. As weights in the cluster analysis, various tables of a.r. [3-7] (group [2]) hydrophobicity known in the literature are used (see Table1 or Table2). Separately, for clustering electrically charged amino acid residues, the function of calculating weighting coefficients as modules of partial charges of side groups according to the formulas, which are derived from the Henderson-Hasselbach equation, is implemented [8]. Alternative: modification interpoint distances, instead clusterization points weights. moddist(u, w) = dist(u, w)/(w u)/2)), where w and u - weighting coefficients of points. As hyperparameters DBSCAN uses t he epsilon neighborhood radius (eps) and the minimum number of neighbors (min_samples). Eps is defined as the maximum distance (in Angstrom (Å)) between the centers of mass of hydrophobic a.r. (or chemical groups) which are adjacent in one cluster. The min_samples/eps³ ratio is proportional to the maximum distribution density of the centers of mass of the hydrophobic a.r. (or chemical groups). Internal clustering validation measures (descibed in Table 3) are used as the quality criteria for cluster analysis. For clusters of complex shape, it is better to use the silhouette coefficient. At the same time, Calinski and Harabasz score, which uses the distance between the element and the center of the cluster, correctly estimates the areas of clusters with the highest density. This areas are of interest from the point of view of the structural organization of proteins. A feature of the DBSCAN algorithm is the strong dependence of clustering results on the parameters - eps and min_samples. Hydrocluster implemented the selection of these parameters by simply iterating over their values at user-defined boundaries, followed by sorting the results according to the criterion of maximizing (minimizing) the value of the corresponding estimated coefficient.

Table 1. Normalised (by Alanine) hydrophobic weights of amino acid residues

a.r.	Hydropathy [3]	Fuzzyoildrop [4]	MENV [5]	Nanodroplet [6]	Aliphatic [7]
ALA	1.0	1.0	1.0	1.0	1.0
VAL	2.333	1.418	2.52	0.867	2.9
LEU	2.111	1.369	2.64	0.904	3.9
ILE	2.5	1.544	2.94	1.016	3.9
PHE	1.556	1.583	2.58	0.963	-
TRP	-	1.497	2.03	0.900	-
MET	1.056	1.448	1.64	0.799	-
CYS	1.389	1.748	3.48	0.588	-
THR	-	0.538	1.82	0.424	-
SER	-	-	-	0.372	-
GLY	-	-	-	0.477	-

Table 2. Hydrophobic weights of chemical (Rekker's) groups [2]

Chemical radical	Hydrophobic weight
C₆H₅ (phenyl)	1.903
CH	0.315
CH₂	0.519
CH₃	0.724
Indolyl	1.903

Table 3. Internal clustering validation measures

Scoring function	Range of values	Optimal value	Realisation	Paper
Calinski-Harabasz score	0 ->	maximum	scikit-learn	[9]
Silhouette score	-1 ... 1	maximum	scikit-learn	[10]
S_Dbw	0 ->	minimum	internal	[11, 12]

Requirements

• Python 3.4 or higher (CPython only support)
• psutil
• progressbar2
• matplotlib>=1.5.1
• numpy>=1.14.2
• scikit_learn>=0.19.1
• biopython>=1.71
• mmtf-python>=1.1.0
• msgpack>=0.5.6

To easily browse through db files you will need a DB Browser for SQLite (https://sqlitebrowser.org). It is recommended to install Pymol molecular viewer (version: 1.7+).

For MS Windows: Use Anaconda (https://anaconda.org) for Windows - it includes majority of the dependencies required. But mmtf-python and msgpack not available on Anaconda - need to use pip. Define environment variable PYTHONIOENCODING to UTF-8. For correct display of the Angstrom symbol use console fonts including this symbol (for example, SimSun font family).

References

1. Ester, M., H. P. Kriegel, J. Sander, and X. Xu, In: Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining, Portland, OR, AAAI Press,226-231. 1996
2. R. Mannhold, R. F. Rekker Perspectives in Drug Discovery and Design, 18: 1–18, 2000.
3. J. Kyte, R. F. Doolittle. J Mol Biol. 1982. 157, 105-132.
4. Brylinski M, Konieczny L, Roterman I. Int J Bioinform Res Appl. 2007;3(2):234-60.
5. D. Bandyopadhyay .E. L. Mehler.Proteins 2008.72.646-659
6. Zhu C. Q., Gao Y. R. , Li H. et.al.// Proc. NAS. 2016.113.12946.
7. Ikai, A.J. 1980. J. Biochem. 88, 1895-1898.
8. Dexter S. Moore BIOCHEMICAL EDUCATION 13(1) 1985.
9. Calinski T., Harabasz J. // Communications in Statistics. 1974. 3 . 1.
10. Rousseeuw P. Comput. Appl. Math. 1987. 20. 53.
11. M. Halkidi and M. Vazirgiannis, in ICDM, Washington, DC, USA, 2001, pp. 187–194.
12. Tong, J. & Tan, H. J. Electron.(China) (2009) 26: 258. https://doi.org/10.1007/s11767-007-0151-8