1. Single-Nucleotide RNA and Ribose Loop Closure Subroutines
DESCRIPTION:
Fortran 77 and ANSI C subroutines to reclose single-nucleotide loops and riboses in RNAs or DNAs.
REFERENCE:
C.H. Mak, "RNA conformational sampling: I. Single-Nucleotide Loop Closure", J. Comput. Chem., Vol. 29, p.926-933, 2008.
LICENSE: GPL
VERSION: N/A RELEASED: 2007/01 | Download |2. Multi-Nucleotide RNA Loop Closure Subroutines
DESCRIPTION:
Fortran 77 and ANSI C subroutines to reclose arbitrary-length multi-nucleotide loops in RNAs or DNAs.
REFERENCE:
C.H. Mak, W.-Y. Chung and N.D. Markovskiy, "RNA conformational sampling: II. Multi-Nucleotide Loop Closure", J. Chem. Theo. Comput., 7(4) 1198-1207 (2011).
LICENSE: See README file
VERSION: N/A RELEASED: 2011/03 | Download |
3. Coming Soon! Loops MC: All-Atom RNA Monte Carlo Simulation Program
DESCRIPTION:
All-atom Monte Carlo simulation program for RNAs using generalized loop closure. (Compile with Tinker Library.)
REFERENCE:
C.H. Mak, "Loops MC: A Monte Carlo simulation program for RNA using generalized loop closure", Mol. Simulat., (submitted 2010).
LICENSE: GPL
VERSION: N/A RELEASED: 2011/03 | Download |
4. Chemical Kinetics Simulation
DESCRIPTION:
Excel spreadsheet for chemical kinetics simulation. Up to 10 species and 8 reactions, any order, any stoichiometry. Solution is obtained by integrating the master equations using simple forward-differencing. Note: User must check convergence manually by decreasing time step. Solution is prone to numerical problems for stiff systems.
LICENSE:
This software comes with no warranty, expressed or implied. Use at your own risk.
VERSION: N/A RELEASED: 2009/12 | Download |