README
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Program: PROPAB v1.0 (c)amal kumar bandyopadhyay and associated workers
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Version: (c) v1.0
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Author:
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Parth Sarthi Sen Gupta, Department of Chemistry, IISER, Berhampur, Berhampur, Ganjam, odisha, 760010, India;
Rifat Nawaz UL Islam, Department of Zoology, The University of Burdwan, West Bengal, 713104, India;
Debanjan Roy, Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
Chittran Roy, Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
Shyamashree banerjee, Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
Sahini Banerjee, Department of Biotechnology, Institute of Genetic Engineering, West Bengal, 700128, India
AMAL K Bandyopadhyay, Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India
Correspondence: akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;
Input: PDB file (crystallographic format) in .pdb or .ent format (available at RCSB/ePDB/jPDB)
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WHAT PROPAB DOES
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OUTPUTS for 2AZ3.pdb
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2az2_result.txt----------------step-by-step computation of propensity
FASTA_ALL_PDB_ALL_SEGMENTs.txt-all segments FASTA files
RSP_COIL.xls-------------------propensity, %composition, physiochemical properties chain, range, all PDB specific
RSP_HELIX.xls------------------as above for HELIX only
RSP_STRAND.xls-----------------as above for STRAND only
RSP_SEGMENT_PHYCO.xls----------chain and all PDB specific physiochemical properties
In them:
** it uses crystallographic files to calculate residue PROPENSITY
** The program extracts and demonstrate step-by-step extraction of sec information
part of the output is as below (file: "PDB_result.txt"):
Topology scan for HELIX ...DONE
A-chain; 152-amino acids; 10 HELIX
1] K 13-R 19 7
2] L 21-K 32 12
......
.....
B-chain; 151-amino acids; 9 HELIX
1] K 13-R 19 7
2] L 21-K 32 12
....
....
Topology scan for STRAND ...DONE
A-chain; 152-amino acids; 4 STRAND
1] R 7-V 12 6
2] K 35-M 42 8
....
....
B-chain; 151-amino acids; 4 STRAND
1] R 7-V 12 6
2] K 35-M 42 8
.....
....
extract seq for HELIX ...DONE
A-chain:82 residues, 10 HELIX
1] KPDGVQR
2] LIGDIVTRLETK
.....
....
B-chain:77 residues, 9 HELIX
1] KPDGVQR
2] LIGDIVTRLETK
.....
.....
extract seq for STRAND ...DONE
A-chain:24 residues, 4 STRAND
1] RTFVMV
2] KMVGGKFM
.....
....
etc
TABLE:
COMPOSITION, BETA, ALFA AND RANDOM COIL PROBABILITY
A(152)-chain:
Non-polar 58 38.16%
Polar 94 61.84%
HRK 21 13.82%
DE 17 11.18%
NQ 07 4.61%
ST 11 7.24%
MC 5 3.29%
M 05 3.29%
C 00 0.00%
SEQ A(152):- [: BETA: 4 (24) 15.79% :] [: ALFA: 10 (82) 53.95% :] [: Random coil: 30.26% :
AA TOTAL % A #(A) R(A) AV(A) P(A) B #(B) R(B) AV(B) P(B) C #(C) R(C) AV(C) P(C)
VAL 11 7.24 V 5 0.45 0.52 0.88 V 5 0.45 0.16 2.81 V 1 0.09 0.27 0.34
ALA 13 8.55 A 9 0.69 0.52 1.34 A 1 0.08 0.16 0.48 A 3 0.23 0.27 0.85
PHE 8 5.26 F 5 0.62 0.52 1.21 F 3 0.38 0.16 2.32 F 0 0.00 0.27 0.00
ILE 7 4.61 I 5 0.71 0.52 1.38 I 1 0.14 0.16 0.88 I 1 0.14 0.27 0.53
LEU 10 6.58 L 6 0.60 0.52 1.16 L 0 0.00 0.16 0.00 L 4 0.40 0.27 1.48
MET 5 3.29 M 1 0.20 0.52 0.39 M 4 0.80 0.16 4.94 M 0 0.00 0.27 0.00
CYS 0 0.00 C 0 0.00 0.52 0.00 C 0 0.00 0.16 0.00 C 0 0.00 0.27 0.00
ASP 19 12.50 D 8 0.42 0.52 0.81 D 0 0.00 0.16 0.00 D 11 0.58 0.27 2.14
GLU 14 9.21 E 8 0.57 0.52 1.11 E 1 0.07 0.16 0.44 E 5 0.36 0.27 1.32
ASN 3 1.97 N 1 0.33 0.52 0.64 N 0 0.00 0.16 0.00 N 2 0.67 0.27 2.46
GLN 4 2.63 Q 4 1.00 0.52 1.93 Q 0 0.00 0.16 0.00 Q 0 0.00 0.27 0.00
LYS 5 3.29 K 2 0.40 0.52 0.77 K 2 0.40 0.16 2.47 K 1 0.20 0.27 0.74
ARG 9 5.92 R 6 0.67 0.52 1.29 R 1 0.11 0.16 0.69 R 2 0.22 0.27 0.82
HIS 7 4.61 H 3 0.43 0.52 0.83 H 1 0.14 0.16 0.88 H 3 0.43 0.27 1.58
SER 4 2.63 S 2 0.50 0.52 0.97 S 0 0.00 0.16 0.00 S 2 0.50 0.27 1.85
THR 7 4.61 T 5 0.71 0.52 1.38 T 1 0.14 0.16 0.88 T 1 0.14 0.27 0.53
TRP 3 1.97 W 1 0.33 0.52 0.64 W 1 0.33 0.16 2.06 W 1 0.33 0.27 1.23
TYR 3 1.97 Y 3 1.00 0.52 1.93 Y 0 0.00 0.16 0.00 Y 0 0.00 0.27 0.00
PRO 4 2.63 P 1 0.25 0.52 0.48 P 0 0.00 0.16 0.00 P 3 0.75 0.27 2.77
GLY 16 10.53 G 7 0.44 0.52 0.85 G 3 0.19 0.16 1.16 G 6 0.38 0.27 1.38
then
B-chain;
C-chain etc
all PDBs etc
** it extracts sequence of TOTAL, STRAND, HELIX, COIL segments and
write them in FASTA format. seq of all chains, all PDBs are extracted
file: "FASTA_ALL_PDB_ALL_SEGMENTs.txt"
** prepares chain-specific, PDB-specific RANGE-specific propensity
TABLEs for STRAND, HELIX, COIL in EXCEL format
** in the above tables, PROPAB smartly overcast %-compositions for those
residues that show appearance in these propensity tables
ranges are
0.0 (no propensity) name residues
>=1.0 (all residues in one column)
1.0 - 1.5
1.5 - 2.0
2.0 - 2.5
2.5 - 3.0
3.0 - above
Files: "RSP_STRAND.xls"; RSP_HELIX.xls; RSP_COIL.xls
[RSP: range specific propensity]
** Segment specific certain PHYSICOCHEMICAL PROPERTIES (GRAVY, ALIPHATIC
INDEX and pI) are also included in these files.
** Separate excel output for PHYSICOCHEMICAL PROPERTIES (GRAVY, ALIPHATIC
INDEX and pI) in chain specific, PDB specific manner
file:"SEGMENT_PHYCO.xls"
INSTRUCTION:
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THE PROGRAM IS EXTENSIVELY TESTED TO FUNCTION ON CYGWIN WITH both C-SHELL/B_SHELL
1. Download PROPAB ("propab.zip") from its home page -- << sourceforge.net >>
2. unzip the content - README (this file) and "WORK"-directory will be visible with two sample pdb files (2az3.pdb)
3. 'cd' to "WORK" directory.
4. In SHELL prompt type ./PROPAB.exe
WHAT PLATFORMS ARE SUPPORTED?
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The program is repeatedly tested for its functionality in CYGWIN-32bit UNIX like environments
using C-SHELL. However, it should work in other UNIX platforms. In case of problems users
may contact above e.mail
The program is interpreted by AWK programming language:
developed by - Aho AV, Kernighan BW, Weinberger PJ 1977
LICENSING
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The program PROPAB (c)v1.0 permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly credited.
This is distributed under the terms of the Creative Commons Attribution License.
FEEDBACK
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problems, bugs , suggestions are requested to be dropped in the above e.mail ie
akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;
FURTHER WORK
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NMR and other structure files are to be included in the processing circle of PROPAB
along with inclusion of active site information in structure files
India, April, 2018
END of README
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PROPAB.zip (405.0 kB)
