DINOSAUR

A set of programs for structure refinement using direct NOE restraints.

Alexandre Bonvin
NMR Spectroscopy Group
Bijvoet Center for Biomolecular Research, Utrecht University,
The Netherlands.

Details

Optaining DINOSAUR

To optain DINOSAUR please download the license agreement and mail or fax the signed form to:

Prof. Dr. R. Boelens
Department of NMR Spectroscopy - Bijvoet Center for Biomolecular Research
Utrecht University 
Padualaan 8
3584 CH Utrecht 
The Netherlands 
Fax: +31 30 2537623
Email : boelens@nmr.chem.uu.nl

DINOSAUR is a set of programs for structure refinement using direct NOE restraints. The following procedures are defined :

Procedures creating the necessary files:

  • DINOIN: creates or modifies the DINOSAUR input file
  • MKHTYP: creates a proton codes file for the GROMOS programs (DINOEM and DINOMD).
  • MKHCO: creates a proton only file (.mdh) or a proton trajectory file (.hco) from GROMOS coordinates or trajectory files
  • CVNOE: conversion program for NOE trajectories: binary <--> formatted
  • CVHCO: conversion program for proton trajectories: binary <--> formatted


Special for ensemble refinement:

  • GENENS: generates a GROMOS file containing several solutes (ensemble) by duplicating and shifting one solute or by combining several different solutes.
  • SPLITCO: inverse of GENENS, splits ensemble coordinates files into several files with each one solute molecule.
  • AVNOE: averages NOE trajectories for analysis with ANANOE


Simulation/refinement procedures:

  • DINODD: NOEs driven dynamics. This program is based on program SHAKE (distances driven dynamic) of Ruud Scheek University of GRONINGEN and works with DG format files.
  • DINOEM: NOEs restrained energy minization based on the GROMOS program PROEML
  • DINOMD: NOEs restrained molecular dynamic based on the GROMOS program PROMDL


Analysis procedures:

  • RFACAV: Calculation of a set of R-factors from a proton trajectory file.
  • RFACDG : Calculation of a set of R-factors for DG structures.
  • RFACGR : Calculation of a set of R-factors for GROMOS structures.
  • RFACDIS : Calculation of a set of R-factors for DISCOVER structures.
  • RFACPDB : Calculation of a set of R-factors for PDB structures.
  • RNOISE : Calculation of R-factors as function of the experimental errors defined as (NOISE + %err * Aexp)
  • SELPKS : Selection of NOE peaks from input file for analysis with ANANOE (only for 2D DINOSAUR)
  • SELDIM : In case of symetrical dimer, SELDIM selects NOEs from the DINOSAUR input file, duplicates and writes them to a NOE file which can be read in DINOIN. By comparing the theoretical NOE intensities for both possible assignments with the experimental ones a choice can be made if the NOE is intra- or inter- monomer.
  • CHAMB : In case of a symetrical dimer CHAMB check the assignments by comparing the distances and NOEs for both possible assignments (inter or intra monomer). It uses therefore a distance file genrated by the Rfactor calculation and a NOE energy file generated by ANANOE.
  • ANANOE : Analysis of a NOE trajectory in terms of R-factors, residue R-factors, NOE energies ... for a set of selected peaks.
  • CHKASS : Analysis of the results of the dynamic assignment procedure implemented in DINOSAUR


Special 3D NOE-NOE refinement:

  • GEN3DDIS: Generates qualitative distance constraints from 3D NOE-NOE data

For a normal run:

 

source dinosaur (instal DINOSAUR procedures)

  • (source ~albo/dino/csh/dinosaur)

dinoset (define molecule name)

dinodir (define or modify working directory)

dinoin (create or modify input file)

dinodd (refinement step)

  • or dinomd
  • or dinoem

rfacav (analysis - R-factors)

  • or rfacdg
  • or rfacgr
  • or rfacdis
  • or rfacpdb

selpks (selection of NOE peaks)
ananoe (analysis NOE trajectory)

References:

  • A.M.J.J. Bonvin, R. Boelens and R. Kaptein "Direct NOE refinement of biomolecular structures using 2D NMR data." J. Biomol. NMR 1, 305-309 (1991).
  • A.M.J.J. Bonvin, R. Boelens and R. Kaptein "Time- and ensemble-averaged direct NOE restraints." J. Biomol. NMR 4, 143-149 (1994).
  • A.M.J.J. Bonvin "Determination of biomolecular structures by NMR. Use of relaxation matrix calculations." PhD Thesis, Utrecht University (1993) ISBN 90-393-0408-4.