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.