Protein Dynamics Software

These programs written in Matlab or Java are available for free download.

  

RELAXFIT
A program for extracting relaxation rates (e.g. R1 or R2) from fitting experimental data to an exponentially decaying function.
Reference: Fushman et al., J. Mol. Biol. 266 (1997) 173.

download  
  

DYNAMICS
A program for model-free analysis of 15N relaxation data.
Features isotropic, axially-symmetric and fully anisotropic models for the overall tumbling of the molecule, and monomer-dimer equilibration. Allows input of site-specific 15N CSA values or their determination, together with model-free parameters, when relaxation data at multiple fields are available.

References: Fushman et al., J. Mol. Biol. 266 (1997) 173; J.B.Hall & D.Fushman, J. Biomol. NMR (2003) 27, 261; J.B.Hall & D.Fushman, J. Amer. Chem. Soc. (2006) 128, 7855-7870; D.Fushman, "Determining protein dynamics from 15N relaxation data by using DYNAMICS", in Protein NMR Techniques, Third Edition, Eds. A. Shekhtman, D. S. Burz, Methods in Molecular Biology, 2012, Volume 831, 485-511, Springer Science, DOI: 10.1007/978-1-61779-480-3_24.

download  
  

ROTDIF
A program for determining the overall rotational diffusion tensor of a molecule from spin-relaxation data.
Features isotropic, axially-symmetric, and fully anisotropic models for the overall motion.

Reference: Fushman et al., Biochemistry 38 (1999) 10225-10230; Varadan et al., JMB 324 (2002) 637; Walker et al. J. Magn. Reson. (2004) 168, 336; Fushman et al, Progress NMR Spectroscopy, (2004) 44, 189.

for Matlab 7 and newer versions for Matlab 6.5 and older versions
  

ROTDIF 3
A redesigned version of the program ROTDIF for determining the overall rotational diffusion tensor of a molecule from spin-relaxation data.
This version is written in Java and features a Graphical User Interface. Allows analysis of 15N and 13C relaxation data, separately or together, at a single or multiple fields, for proteins and/or nucleic acids. Also estimates model-free parameters. Features isotropic, axially-symmetric, and fully anisotropic models for the overall motion. The program also includes modules for prediction of the rotational diffusion tensor from atom coordinates using ellipsoid model (ELM), and for diffusion-tensor-based rigid-body docking of macromolecules (ELMDOCK).

Reference: K.Berlin, A.Longhini, T.K.Dayie, D.Fushman, J Biomol NMR (2013), 57, 333-352.

link to Java version download  
  

SES
A program for recovering a representative conformational ensemble of a macromolecule from (underdetermined) experimental data using sparce-ensemble selection (SES) combined with multi-orthogonal matching pursuit (Multi-OMP). Currently features analysis of residual dipolar coupling (RDC) data.
Reference: Berlin et al., JACS 135 (2013) 16595.

link to Java version download  
  

ALTENS
A program for determining the alignment tensor of a molecule from residual dipolar coupling (RDC) data, using singular value decomposition.
Reference: Varadan et al., JMB 324 (2002) 637; Fushman et al, Progress NMR Spectroscopy, (2004) 44, 189.

download  
  

PATI
A program for predicting the alignment tensor of a molecule and the residual dipolar couplings (RDCs) under steric alignment caused by planar objects, and for determining the alignment tensor from experimental RDC data using singular value decomposition.
Features isotropic, axially-symmetric, and fully anisotropic models for the overall motion. The program also includes a module for alignment-tensor-based rigid-body orientation and docking of macromolecules (PATIDOCK)

Reference: K.Berlin, D.P.O’Leary, D.Fushman, J. Magn. Reson (2009) 201, 25-33.

link to Java version download  
   JCSA
A program for determining the spectral densities, J(w), and the 15N chemical shift anisotropy from the field dependence of 15N relaxation rates, R2, R1, and NOE. Requires relaxation data measured at 2 or more fields.
Features various methods of analysis, including independent assessment of the conformational exchange term, Rex.

Reference: Fushman et al., J. Amer. Chem. Soc. 121 (1999) 8577-8582.
zip  

ETAFIT
A program for the determination of the magnitude and orientation of the 15N chemical shift anisotropy from the field dependence of the ratio, h /R2, of the CSA/dipolar cross-correlation term h and the 15N transverse relaxation rate R2. Requires relaxation data measured at 2 or more fields.
Reference: Fushman et al., J. Amer. Chem. Soc. 120 (1998) 10947-10952.

zip   

PICK
A program for automatic peak picking in a 2D spectrum given a reference peak list.
Features reading-in spectra produced with TopSpin and full peak-list export/importability with CARA. Converts between CARA and Sparky peak lists.

zip  

KdFit
A program for determining dissociation constants from analysis of titraton data from NMR or fluorescence anistropy. Fits titration data to various stoichiometry models. Ligand-binding models currently included: single-site binding; two binding sites with independent or mutually-exclusive binding.
Reference: Varadan et al., J. Biol. Chem. 279 (2004) 7055-7063.

zip  

SLFit
A program for determining the coordinates of a paramagnetic spin label based on paramagnetic relaxation enhancement (PRE) effect measurements.
Reference: Ryabov & Fushman, Proteins 63 (2006) 787-796.

zip