HBPLUS v 2.19 - Free Hydrogen Bond Calculator
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HBPLUS is a hydrogen bond calculation program that has been developed
in-house over the course of over four years and has been used in countries
as distant as the USA, Taiwan and South Africa. It calculates positions
for polar hydrogens, which it can output in PDB format. It can also be
used to generate a list of neighbour interactions.
In the process of the algorithm, it calculates the angles at the hydrogen
and the acceptor as well as the donor-acceptor and hydrogen-acceptor
distances. All the hydrogen bond criteria, including which atoms do or do
not hydrogen bond, are customisable.
The program inputs a Brookhaven protein database format file, and outputs a
list of hydrogen bonds, including geometries.
It is written in ANSI C and has been checked on several UNIX systems as
well as VAX/VMS. It requires too much memory to run on an IBM PC.
If you would like a copy of HBPLUS, simply snailmail me a signed copy of
the confidentiality agreement at the bottom of this post and I shall email
you the source code and documentation. The agreement boils down to you
promising not to give anyone outside your lab copies, and to reference us
if you use HBPLUS' results in a paper. HBPLUS is free to academic users.
HBPLUS is (c) IK McDonald, D Naylor, D Jones and JM Thornton 1993
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Correspondence to:
Ian McDonald (PG)
Biological Structure and Modelling Unit
Department of Biochemistry and Molecular Biology
University College London
Gower Street
LONDON WC1E 6BT
UK / EC
Email mcdonald at uk.ac.ucl.biochemisty.bsm
HBPLUS - Hydrogen Bond Calculation
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CONFIDENTIALITY AGREEMENT
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In regard to the HBPLUS program, specified in Appendix 1 herewith (the
Software) supplied to us, the copyright and other intellectual property
rights to which belong to the authors, we
__________________________________________________________________
undertake to the authors that we shall be bound by the following terms and
conditions:-
1. We will receive the Software and any related documentation in confidence
and will not use the same except for the purpose of the department's own
research. The Software will be used only by such of our officers or
employees to whom it must reasonably be communicated to enable us to
undertake our research and who agree to be bound by the same confidence.
The department shall procure and enforce such agreement from its staff for
the benefit of the authors.
2. The publication of research using the Software must reference "McDonald
IK, Naylor DN, Jones DT & Thornton J M (1993), 'HBPLUS', Computer Program,
Department of Biochemistry and Molecular Biology, University College
London." or successor references as defined by the authors.
3. Research shall take place solely at the department's premises at
__________________________________________________________________
4. All forms of the Software will be kept in a reasonably secure place to
prevent unauthorised access.
5. Each copy of the Software or, if not practicable then, any package
associated therewith shall be suitably marked (and such marking maintained)
with the following copyright notice: "Copyright 1991-3 Ian McDonald, Dorica
Naylor, David Jones and Janet M Thornton All Rights Reserved".
6. The Software may be modified but any changes made shall be made
available to the authors.
7. The Software shall be used exclusively for academic teaching and
research. The Software will not be used for any commercial research or
research associated with an industrial company.
8. The confidentiality obligation in paragraph one shall not apply:
(i) to information and data known to the department at the time of
receipt hereunder (as evidenced by its written records);
(ii) to information and data which was at the time of receipt in the
public domain or thereafter becomes so through no wrongful act of
the department;
(iii) to information and data which the department receives from a third
party not in breach of any obligation of confidentiality owed to
the authors.
Please sign this Undertaking and return a copy of it to indicate that you
have read, understood and accepted the above terms.
For and on behalf of _____________________________
_________________________________________________
..................................................
Email ............................................
Dated ............................................
APPENDIX 1 - DETAILS OF THE HBPLUS PROGRAM PROVIDED
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Files to be included
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1. hbplus.c } Source program file
2. hbplus.man } Documentation
