Literature DB >> 21132109

Browndye: A Software Package for Brownian Dynamics.

Gary A Huber1, J Andrew McCammon.   

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.

Entities:  

Year:  2010        PMID： 21132109      PMCID： PMC2994412          DOI： 10.1016/j.cpc.2010.07.022

Source DB:  PubMed          Journal:  Comput Phys Commun        ISSN： 0010-4655            Impact factor:   4.390


  14 in total

1.  Electrostatic dependence of the thrombin-thrombomodulin interaction.

Authors:  A Baerga-Ortiz; A R Rezaie; E A Komives
Journal:  J Mol Biol       Date:  2000-02-18       Impact factor: 5.469

2.  Translational friction coefficients for cylinders of arbitrary axial ratios estimated by Monte Carlo simulation.

Authors:  Steen Hansen
Journal:  J Chem Phys       Date:  2004-11-08       Impact factor: 3.488

3.  Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.

Authors:  Chia-En Chang; Tongye Shen; Joanna Trylska; Valentina Tozzini; J Andrew McCammon
Journal:  Biophys J       Date:  2006-03-13       Impact factor: 4.033

4.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

5.  Weighted-ensemble Brownian dynamics simulations for protein association reactions.

Authors:  G A Huber; S Kim
Journal:  Biophys J       Date:  1996-01       Impact factor: 4.033

6.  Reduced surface: an efficient way to compute molecular surfaces.

Authors:  M F Sanner; A J Olson; J C Spehner
Journal:  Biopolymers       Date:  1996-03       Impact factor: 2.505

7.  A simplified representation of protein conformations for rapid simulation of protein folding.

Authors:  M Levitt
Journal:  J Mol Biol       Date:  1976-06-14       Impact factor: 5.469

8.  Simulation of the diffusional association of barnase and barstar.

Authors:  R R Gabdoulline; R C Wade
Journal:  Biophys J       Date:  1997-05       Impact factor: 4.033

Review 9.  Classical electrostatics in biology and chemistry.

Authors:  B Honig; A Nicholls
Journal:  Science       Date:  1995-05-26       Impact factor: 47.728

10.  Simulation of enzyme-substrate encounter with gated active sites.

Authors:  R C Wade; B A Luty; E Demchuk; J D Madura; M E Davis; J M Briggs; J A McCammon
Journal:  Nat Struct Biol       Date:  1994-01
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  42 in total

1.  Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.

Authors:  Patricia Bauler; Gary A Huber; J Andrew McCammon
Journal:  J Chem Phys       Date:  2012-04-28       Impact factor: 3.488

2.  Assessing the two-body diffusion tensor calculated by the bead models.

Authors:  Nuo Wang; Gary A Huber; J Andrew McCammon
Journal:  J Chem Phys       Date:  2013-05-28       Impact factor: 3.488

3.  SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

Authors:  Lane W Votapka; Benjamin R Jagger; Alexandra L Heyneman; Rommie E Amaro
Journal:  J Phys Chem B       Date:  2017-03-03       Impact factor: 2.991

4.  Substrate channeling between the human dihydrofolate reductase and thymidylate synthase.

Authors:  Nuo Wang; J Andrew McCammon
Journal:  Protein Sci       Date:  2015-06-29       Impact factor: 6.725

5.  Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism.

Authors:  Sophia P Hirakis; Robert D Malmstrom; Rommie E Amaro
Journal:  Biochemistry       Date:  2017-07-17       Impact factor: 3.162

6.  Molecular analysis of the interaction between staphylococcal virulence factor Sbi-IV and complement C3d.

Authors:  Ronald D Gorham; Wilson Rodriguez; Dimitrios Morikis
Journal:  Biophys J       Date:  2014-03-04       Impact factor: 4.033

7.  Cardiac myosin activation with 2-deoxy-ATP via increased electrostatic interactions with actin.

Authors:  Joseph D Powers; Chen-Ching Yuan; Kimberly J McCabe; Jason D Murray; Matthew Carter Childers; Galina V Flint; Farid Moussavi-Harami; Saffie Mohran; Romi Castillo; Carla Zuzek; Weikang Ma; Valerie Daggett; Andrew D McCulloch; Thomas C Irving; Michael Regnier
Journal:  Proc Natl Acad Sci U S A       Date:  2019-05-20       Impact factor: 11.205

8.  Improvements to the APBS biomolecular solvation software suite.

Authors:  Elizabeth Jurrus; Dave Engel; Keith Star; Kyle Monson; Juan Brandi; Lisa E Felberg; David H Brookes; Leighton Wilson; Jiahui Chen; Karina Liles; Minju Chun; Peter Li; David W Gohara; Todd Dolinsky; Robert Konecny; David R Koes; Jens Erik Nielsen; Teresa Head-Gordon; Weihua Geng; Robert Krasny; Guo-Wei Wei; Michael J Holst; J Andrew McCammon; Nathan A Baker
Journal:  Protein Sci       Date:  2017-10-24       Impact factor: 6.725

9.  Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research.

Authors:  Ahmet Erdemir; Peter J Hunter; Gerhard A Holzapfel; Leslie M Loew; John Middleton; Christopher R Jacobs; Perumal Nithiarasu; Rainlad Löhner; Guowei Wei; Beth A Winkelstein; Victor H Barocas; Farshid Guilak; Joy P Ku; Jennifer L Hicks; Scott L Delp; Michael Sacks; Jeffrey A Weiss; Gerard A Ateshian; Steve A Maas; Andrew D McCulloch; Grace C Y Peng
Journal:  J Biomech Eng       Date:  2018-02-01       Impact factor: 2.097

10.  Electrostatic control of calcineurin's intrinsically-disordered regulatory domain binding to calmodulin.

Authors:  Bin Sun; Erik C Cook; Trevor P Creamer; Peter M Kekenes-Huskey
Journal:  Biochim Biophys Acta Gen Subj       Date:  2018-07-31       Impact factor: 3.770
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