README
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Program:
=======
ADSBET - Automated Determination of Salt-bridge Energy Terms
Version:--1
April, 2014
Authors:
=======
Arnab Nayek, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Sunit Das, Vishma Pratap Sur,
Pratay Seth, Rifat Nawaz Ul Islam and Amal K bandyopadhyay*
Address:
=======
Department of Biotechnology,The University of Burdwan, WB, India
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FEATURES AND FUNCTION:
=====================
ADSBET performs following steps for computation of net as well as component energy terms
-- Determination of residue specific salt-bridges or ion-pairs from crystal structures
-- Determination of protein specific center of mass; needed for desolvation energy computation
-- Determination of protein specific grid points (along x, y and z dimension) to be used in APBS calculation
-- Preparation of PQR (protein charge-radius) file from pdb file (using PDB2PQR)
-- generation of hydrophobic isosteres mutated PQR files (5 per salt bridge )
These are needed for computation of electrostatic field energy
-- Preparation of APBS input file using modified PQR file plus user, default and generated parameters.
-- run of APBS and computation of component energy terms
-- Redirection of all energy terms in compact excel format
INPUT:
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Cryatal structure in PDB format (RCSB)
If minimized user to keep all header info as is the original PDB.
OUTPUT:
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one compact output named "all_sb_eng_table.xls" in the working directory
PLATFORM
========
The program works in any UNIX environment including CYGWIN. It is extensively tested to function properly
from CYGWIN environment.
INSTALLATION:
============
THE PROGRAM IS EXTENSIVELY TESTED TO FUNCTION ON CYGWIN WITH both in C-SHELL/B-SHELL
1. Download ADSBET ("ADSBET.zip") from its home page -- << sourceforge.net >>
2. unzip the content - README (this file) and "WORK"-directory will be
visible with sample pdb & pqr files (1CZP.pdb,1CZP.pqr)
3. Open a Shell (C- or B-SHELL in CYGWIN) and 'cd' to "WORK" directory of "adsbet.exe"
4. In SHELL prompt type "./adsbet.exe h" OR "./adsbet.exe"
INSTALLATION OF OTHER PROGRAMS NEEDED for ADSBET
===================================================
1. ADAPTIVE POISSON-BOLTZMAN SOLVER ie "APBS v1.4" to be installed/unzipped in the defined directory:
DIRECTORY: "program-working-directory/afp/apbs"
[available at : http://sourceforge.net/projects/apbs/files/apbs/apbs-1.4.0/ ]
2. "PDB2PQR v1.9" to be installed/unzipped in the defined directory
DIRECTORY: "program-working-directory/afp/pqr
[available at : http://sourceforge.net/projects/pdb2pqr/files/pdb2pqr/pdb2pqr-1.9.0/ ]
NOTE: ADSBET USE SBION AND SBION2 FOR EXTRACTION OF ATOMIC AND RESIDUE SPECIFIC SALT BRIDGES
FROM CRYSTAL STRUCTURE. IT ALSO USED THE SAID PROGRAMS FOR CORRECTION OF PDB FILES EXCLUSIVELY
NEEDED FOR CORRECTNESS OF ENERGY TERMS. USERS ARE REQUIRED TO CITE THESE FOR THEIR USE OF ADSBET.
IMPORTANT CITATIONS:
==================
NOTE : The program ADSBET use "APBS v1.4 (binary)", "PDB2PQR v1.9 (binary)"
and "SBION2"/"SBION" for proper functioning ;
Users of ADSBET are needed to cite following references for their work:
APBS Adaptive Poisson-Boltzmann Solver; Version 1.4.1 [solving PBE]
1] Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems:
application to microtubules and the ribosome. PNAS USA 98, 10037-10041 2001,
PDB2PQR version 1.9 [generation of pqr file:A python-based structural conversion utility]
2] Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for
the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 2004
SBION version 1.0 [obtaining atomic protein specific salt-bridges]
3] SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files,
Parth Sarthi Sen Gupta, Sudipta Mondal, Buddhadev Mondal, Rifat Nawaz Ul Islam,
Shyamashree Banerjee & Amal K Bandyopadhyay
Bioinformation 10 03: 164-166 2014
SBION2 version 2.0 [obtaining residue specific salt-bridges, bond multiplicity and average distance]
4] SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2
Parth Sarthi Sen Gupta, Arnab Nayek, Shyamashree Banerjee1, Pratyay Seth,
Sunit Das, Vishma Pratap Sur, & Amal K Bandyopadhyay
Bioinformation 11 01: 39-42 2015
==================================================================================
*********APBS LICENSE AGREEMENT******************************
----------------------------------------------------------------------
APBS -- Adaptive Poisson-Boltzmann Solver
Version 1.4.1-binary
Nathan A. Baker (nathan.baker@pnnl.gov)
Pacific Northwest National Laboratory
Additional contributing authors listed in the code documentation.
Copyright (c) 2010-2014 Battelle Memorial Institute. Developed at the Pacific
Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific
Northwest Division for the U.S. Department of Energy.
Portions Copyright (c) 2002-2010, Washington University in St. Louis.
Portions Copyright (c) 2002-2010, Nathan A. Baker.
Portions Copyright (c) 1999-2002, The Regents of the University of California.
Portions Copyright (c) 1995, Michael Holst.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the developer nor the names of its contributors may be
used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------------------------------------------------
=========================================================================================
ENERGY MINIMIZATION OF PDB FILES:
================================
SALT BRIDGE ENERGY-TERMS GIVE BEST RESULT WHEN PDB STRUCTURE FILES ARE
SUBJECTED TO ENERGY MINIMIZED. THIS STEP HAS TO BE DONE WITH CAUTION.
HELIX and SHEET INFORMATION ARE TO BE RETAINED in MINIMIZED FILE AS ORIGINAL
PDB FILES.
FEEDBACK:
========
Encouragement, suggestions, bug reports, and constructive criticism
may be sent to akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;. we will do our best
to reach with possible solution as sooner as we can.
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APPENDIX:
=========
UNZIP of "ADSBET.zip"
will produce
1. README (this file)
2. ADSBET.exe
3 "afp" directory -- contains subdirs --"apbs", "pqr", "exedir", "output", "share" and
-- files-- "pdbfilep",pdbfileq","pdbn","progf",progo",progr",progt",progv",progx"
-- "exedir" contains "rd"
-- "output" contains "all_sb_eng_table.xls"
-- "share" contains "glo_f_a.awk"
4. sample files "1CZP.pdb" & 1DOI.pdb
*****************************************************************************
END
Download Latest Version
ADSBET.zip (405.4 kB)
