The following programs developped in our group can be downloaded free of charge for academic purposes. Please click each program name, and input your information. You can obtain the program as informed by E-mail.
Restrained molecular dynamics (MD) with SAXS constraints. All the source codes, manual, and some utility programs are available as a single package. The package does not contain a program to carry out MD itself, and the program can be used in combination with various MD packages. For detailed information, please see J. Appl. Cryst. 37, 103-109 (2004). In version 1.15, calculation in dimensionless scale is possible in order to consider the effect of hydration shell. For example, see Biochem. Biophys. Res. Commun. 431, 65-69 (2013).
Molecular graphics program to visualize molecular structure along with constraint force vectors calculated by SAXS_MD. Source code, manual, and example files are available as an archived file. The program requires OSF Motif and OpenGL environments in its installation and run. For detailed information, please see J. Synchrotron Rad. 15, 535-537 (2008).
Programs for tracing beads in the in the beads-ensemble structure such as that obtained with GASBOR. The programs solve this problem in terms of Graph Theory by finding a Hamilton path, regarding the beads and their neighbouring connections as vertices and edges, respectively. The package contains two programs, MakeEdge and Hamilton-path. MakeEdge lists all the neihbouring connections inside the bead-ensemble structure as 'edge'. Hamilton-path program searches for the Hamilton path to pass over all the beads exactly once by tracing the edges. The former program is written in FORTRAN, and the latter in MIT-Scheme, a dialect of LISP.
SAXSANA program was developed by Dr. Hiragi's group at Kyoto University.
It is an interactive analytical program for SAXS measurements to provide
various tools for the data treatment and analyses. The program supports data
format of BL10C and BL15A of Photon Factory in KEK, but the free format is
also available. SAXSANA was written with Microsoft Visual Basic 5.0 and runs
on Windows platforms. For more detailed information, please see J. Synchrotron
Rad. 10, 193-196 (2003). The package contains all the source codes,
setup.exe, and sample data, and is distributed on this server under the
author's permission.
Program package for analysis of SAXS data such as Guinier, Porod/Luzzati,
and Zimm plots and p(r) calculation. Anarg32n, Porod32n, Zimm32n programs
are QuickWin applications running on Microsoft Windows, and Saxfft3n runs on
N88-BASIC environment/emulator. The manual document is only for Japanese.
This program package is originally intended to use in data treatment at
BL15A of Photon Factory in KEK.
In case of data measured with PSPC, please use PSPC-version.
Now, Web applications translated by JavaScript are also available for
Anarg32 and Porod32. Compared with the original FORTRAN code, inverse
matrices are calculated by Gaussian elimination (row reduction) instead of
Jacobi method (eigenvalue algorithm).
A powerful tool for analyzing polydisperse system. SVD (Singular Value
Decomposition) estimates the number of independent components in the system.
Based on the equilibrium (static) or kinetic model, intrinsic SAXS profile
in each component can be reconstructed. Two- or three-state (sequential)
transition model is supported in static or kinetic analysis. Main routine of
SVD is based on the algorithm in Numerical Recipes in FORTRAN (Cambridge
University Press). Althogh the package is originally intended to analyze
static or kinetic SAXS data for protein unfolding, it may be also applicable
to other experimental method such as CD (circular dichroism) spectroscopy, or
other static/kinetic process accompanying conformational changes.
Program to fit unfolding curve(s) by hybrid (linear and non-linear)
least squares method. It can be used for the conventional analysis to derive
unfolding parameters such as cooperativity and midpoint. The implemented
algorithm is originated from PKAFIT program by Dr. Tanokura at the University
of Tokyo, which was also applied to 'Reconstruction' program listed above.
Web application modified by JavaScript is now available here. Compared
with the original algorithm, non-linear least sqaures are calculated by
downhill simplex method instead of brute force, and inverse matrices are
obtained by Gaussian elimination (row reduction) instead of Jacobi method.