ProDFace

Web-tool for the analysis of Protein-DNA structures (experimental structures, models, MD snapshots, docked structures etc.)

1. INTRODUCTION

ProDFace is a web tool that characterizes the binding region of a protein-DNA complex based on amino acid propensity, hydrogen bond (HB) donor capacity (number of solvent accessible HB donor groups), sequence conservation at the interface core and rim region, and geometry. The program takes as input the structure of a protein-DNA complex in PDB (Protein Data Bank) format, and outputs various physicochemical and geometric parameters of the interface, as well as conservation of the interface residues in the protein component.

2. SYSTEM REQUIREMENT

The web version of ProDFace has been tested in Chrome, Firefox and Edge. However, Java plug-ins should be pre-installed to display Java applets properly. The stand alone version of the program will be released in the next update of ProDFace.

To run different ProDFace components Locally that calculate important parameters, following softwares are required-
i) JDK (Java Development Kit)
ii) C compiler
iii) Perl Compiler (Interpreter)

3. EXTERNAL PROGRAMS

ProDFace uses NACCESS for accessible surface area calculation, DSSP for secondary structure assignments, HBPLUS for hydrogen bond calculation, and PRINCIP and TRANSFORM module from SURFNET to transform the 3D coordinates of the molecules along their principal axes (2D).

4. STEPS FOR RUNNING ProDFace web tool

Step 1

Provide the protein-DNA complex structure by
(a) providing the PDB code (for experimental structures)
OR
(b) uploading your own complex structure (for modelled structures, docking solutions, or MD snapshots) in PDB format.

Step 2

Provide chain ids of the protein and the DNA components that form the interface to be analyzed.

Step 3

Provide the threshold distance for clustering interface atoms into spatial patches (defalut 20 Ang.)

Step 4

Provide Multiple Sequence Alignment (MSA) for the protein component to calculate residue conservation scores by
(a) Using HSSP database
OR
(b) Providing user-defined MSA in FASTA format

5. IMPORTANT ProDFace components

C programs

i) InterfaceConsvSeqIdenArea.c
Calculates conservation score (area normalized shannon entropy) of interface residues
ii) SubunitAvgEntropy_c1.c
Calculates 'average conservation score' of a protein subunit
iii) SecStrClass.c
Calculates percentage of SSE components (helix, strand, Non-regular) of a protein subunit
iv) PPSegment.c
Calculates 'number of interface segments' of a subunit and length of each segment
v) SSSegment.c
Determines SSE of each interface segment

Java programs

i) intDist.java
Calculates distances between all possible interface atom pairs
ii) polar.java
Finds the polar and apolar fraction of an interface
iii) buried.java
Finds fraction of total buried, polar buried, and non-polar buried atoms in an interface
iv) seqres.java
Finds DSSP assigned secondary structure of each interface residue
v) propensity.java
Calculates "Residue Propensity Score" of an interface
vi) localDensity.java
Calculates 'Local Density' of the interface

Perl programs

i) int_water.pl
Calculates Number of interface Waters
ii) Whbs_one_sided.pl
Calculates total No. of water mediated hydrogen bonds formed by an interface
iii) BW_distribution.pl
Calculates total number of Bridging-water and a distribution of total water mediated Hbonds
iv) int_HB_donor_atm_asa.pl
Caclculates accesibility of Hbond donor groups at the interface

If you have any problem or suggestion, please contact: 'contact.arumay @ gmail.com' OR 'sdey @ iitj.ac.in'