BrownDye Citation

@article{ ISI:000282388700010,

Author = {Huber, Gary A. and McCammon, J. Andrew},

Title = {{Browndye: A software package for Brownian dynamics}},

Journal = {{COMPUTER PHYSICS COMMUNICATIONS}},

Year = {{2010}},

Volume = {{181}},

Number = {{11}},

Pages = {{1896-1905}},

Month = {{NOV}},

Abstract = {{A new software package, Browndye, is presented for simulating the

   diffusional encounter of two large biological molecules. It can be used

   to estimate second-order rate constants and encounter probabilities, and

   to explore reaction trajectories. Browndye builds upon previous

   knowledge and algorithms from software packages such as UHBD, SDA, and

   Macrodox, while implementing algorithms that scale to larger systems.

   Program summary

   Program title: Browndye

   Catalogue identifier: AEGT\_v1\_0

   Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGT\_v1\_0.html

   Program obtainable from: CPC Program Library, Queen's University,

   Belfast, N. Ireland

   Licensing provisions: MIT license, included in distribution

   No. of lines in distributed program, including test data, etc.: 143 618

   No. of bytes in distributed program, including test data, etc.: 1 067

   861

   Distribution format: tar.gz

   Programming language: C(++), OCaml (http://caml.inria.fr/)

   Computer: PC, Workstation, Cluster

   Operating system: Linux

   Has the code been vectorised or parallelized?: Yes. Runs on multiple

   processors with shared memory using pthreads

   RAM: Depends linearly on size of physical system

   Classification: 3

   External routines: uses the output of APBS {[}1]

   (http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained

   and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne

   Twister. These are included in the Browndye distribution.

   Nature of problem: Exploration and determination of rate constants of

   bimolecular interactions involving large biological molecules.

   Solution method: Brownian dynamics with electrostatic, excluded volume,

   van der Waals, and desolvation forces.

   Running time: Depends linearly on size of physical system and

   quadratically on precision of results. The included example executes in

   a few minutes.

   References:

   {[}1] N. Baker, D. Sept, S. Joseph, M. Hoist, J. McCammon,

   Electrostatics of nanosystems: Application to microtubules and the

   ribosome, Proc. Natl. Acad. Sci. USA 98 (18) (2001) 10037-10041. (C)

   2010 Elsevier B.V. All rights reserved.}},

Publisher = {{ELSEVIER SCIENCE BV}},

Address = {{PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS}},

Type = {{Article}},

Language = {{English}},

Affiliation = {{Huber, GA (Reprint Author), Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA.

   Huber, GA; McCammon, JA, Univ Calif San Diego, Howard Hughes Med Inst, La Jolla, CA 92093 USA.

   McCammon, JA, Univ Calif San Diego, Ctr Theoret \& Biol Phys, La Jolla, CA 92093 USA.

   McCammon, JA, Univ Calif San Diego, Dept Chem \& Biochem, La Jolla, CA 92093 USA.

   McCammon, JA, Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA.}},

DOI = {{10.1016/j.cpc.2010.07.022}},

ISSN = {{0010-4655}},

Keywords = {{Brownian dynamics; Protein association; Software; Diffusion; Kinetics}},

Keywords-Plus = {{HYDRODYNAMIC INTERACTIONS; SIMULATION; DIFFUSION; ELECTROSTATICS;

   ASSOCIATION; SURFACE; TRANSLATION; HIERARCHIES; PARTICLES; EFFICIENT}},

Subject-Category = {{Computer Science; Physics}},

Web of Science-Category = {{Computer Science, Interdisciplinary Applications; Physics, Mathematical}},

Author-Email = {{This email address is being protected from spambots. You need JavaScript enabled to view it.}},

Funding-Acknowledgement = {{National Institutes of Health; National Science Foundation; Howard

   Hughes Medical Institute; Center for Theoretical Biological Physics at

   UCSD; National Biomedical Computational Resource}},

Funding-Text = {{We are grateful to Maciej Dlugosz for patiently enduring a first draft

   of this software and providing valuable feedback. We also thank Barry

   Grant for being the first user of many of Browndye's features and

   providing more valuable feedback. We thank Adam van Wynsberghe for

   providing the preprocessed thrombin and thrombomodulin PDB files. This

   work has been supported by the National Institutes of Health, National

   Science Foundation, the Howard Hughes Medical Institute, the Center for

   Theoretical Biological Physics at UCSD, and the National Biomedical

   Computational Resource.}},

Number-of-Cited-References = {{46}},

Times-Cited = {{3}},

Journal-ISO = {{Comput. Phys. Commun.}},

Doc-Delivery-Number = {{657CG}},

Unique-ID = {{ISI:000282388700010}},

}