CNS - Crystallography & NMR System
CCP4 (macromolecular crystallography program suite)
DYANA - Program for NMR structure calculation that provides all functionality of its predecessor, DIANA and many new features.
DINOSAUR - Program for structure refinement using direct NOE restraints.
IRMA2 - IRMA procedure calculates distances from experimental NOE spectra with the use of the full relaxation matrix approach.
"O" - Protein crystallographic package
PROTEIN - Program system for the crystal structure analysis of macromolecules.
TALOS - A database system for empirical prediction of phi and psi backbone torsion angles using a combination of five kinds (HA, CA, CB, CO, N) of chemical shift assignments for a given protein sequence.
X-PLOR
2.) Imaging Softwares
OpenDX - (IBM) Visualization Data Explorer
C3D - 3D imaging
NIH-IMAGE - public domain image processing and analysis program for Mac
NIH-IMAGE for windows
3.) Molecular Dynamics softwares
AMBER - Assisted Model Building with Energy Refinement
CHARMM
Discover - Molecular Simulations
GROMOS
MacroModel - Graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution.
NAMD
4.)Molecular Graphics & Visualization Softwares
BRAGI - Interactive protein-modelling program
Cn3D - Allows to view 3-dimensional structures from NCBI's Entrez database
GRASP - Graphical Representation and Analysis of Structural Properties
InsightII - Molecular Simulations
MidasPlus - Molecular Display and Simulation System
MOLDEN - Package for displaying Molecular Density
MSV - Molecular Surface Viewer
MOLMOL
MOLPRO
MOLPRO
MolScript
ORTEP - Crystal Structure Illustrations
PovChem - Molecular graphics software
PREPI - Protein REPresentations Interactively
RasMol
Raster3D - Biomolecular Structure
RIBBONS
SPARTAN - Molecular modelling and visualisation program suite
SPOCK - Molecular graphics program
SYBYL
WebLab Viewer Pro/Lite - Molecular Simulation
WHATIF - 3D modelling services
VMD
5.) NMR processing and analysis softwares
AURELIA - Software for semi-automated analysis of all types of 2D, 3D and 4D spectra.
CORMA (COmplete Relaxation Matrix Analysis) - FORTRAN program for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2DNOE experiment.
CROSREL - Program for the analysis of ROESY and NOESY NMR data.
DASHA - Model-Free Analysis of Protein Dynamics from Heteronuclear NMR Relaxation Data
DSYMPC - NMR SIMULATION AND ITERATION TOOLS FOR PCs
FELIX - NMR data processing, analysis and assignment program (Molecular Simulations).
FIRM - Interactive program for calculating NOEs of a structural model using the relaxation matrix approach. Distances, corrected for the effects of spin diffusion, can be back-calculated from experimetal NOEs using a hybrid relaxation matrix. Includes features for simulating internal motions.
GAMMA - A library written for simulation of Nuclear Magnetic Resonance experiments"
Gifa - A multi-purpose NMR program, designed for the processing, the display and the analysis of 1D, 2D & 3D NMR data-sets.
MARDIGRAS - Matrix Analysis of Relaxation for DIscerning the Geometry of an Aqueous Structure, program for calculating proton-proton distances from cross-peak intensities measured from a 2D NOE experiment.
MestRe-C - A program designed to process and plot 1D NMR spectra on PC’s running Windows 95/98/NT 4.0. It imports files from most spectrometers and includes a number of useful tools .
MEX and CIFIT - For simulation of exchanged-broadened lineshapes for uncoupled spin systems (MEX) and to analyse selective inversion experiments (Hoffman-Forsen) for slow chemical exchange (CIFIT).
Modelfree - Program to fit the extended model free spectral density function to NMR spin relaxation data.
MORASS - Multiple Overhauser Relaxation AnalysiS and Simulation. MORASS uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzes 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained.
NMRPipe - NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis.
NUMARIT - A spin simulation/iteration package for the X32.
PERCH - (PEak reseaRCH) - an integrated NMR-software package for research, analytics and education. The spectral analysis and simulation up to 10 spins is based on the program MLDC (Modified LAOCOON with Dipolar Couplings).
PC Software: APT, DECAY, DEPT, FIDUNK, FTNMR Simulator, HETJ-2D, HOMOJ-2D, IRREADER, NMRSM, UNKINP, XHCORR .
PRONTO - The PROtein Nmr TOol .
RMN - A Nuclear Magnetic Resonance (NMR) data processing program for the Mac.
SIMPSON - (SIMulation Package for SOlid-state Nmr spectroscopy) - A solid-state NMR simulation program with emphasis on ease of use. Multiple pulses, spins, and dimensions. Input files written in Tcl demonstrate simulations of 20 major solid-state experiments.
Sparky - Graphical NMR assignment program for proteins and nucleic acids. Runs under Windows, Linux, or Unix.
SwaN-MR - An NMR processing software for the Macintosh. It reads 1D, 2D, 3D and 4D spectra coming from many spectrometers and its feature list is comparable to those of commercial packages.
V - an interactive software system for MR signal processing. Source
VNMR - Software package for Varian NMR spectrometers.
XEASY - ETH Automated Spectroscopy based on the X Window System to satisfy the requirement for NMR spectrum analysis.
XWIN-NMR - software package sits of BRUKER spectrometers.
6.) Protein & DNA - Structure & Sequence analysis Softwares
CURVES - Helical analysis of irregular nucleic acids
DELILA - Software for Information Analysis of Protein and Nucleic-acid Sequences
DSSP - Protein secondary structure assignment program
Dotter - A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis
Modeller - Program for homology protein structure modelling by satisfaction of spatial restraints
PROCHECK
PROCHECK_NMR
SQUID
7.) Protein properties computation softwares
DelPhi - Finite Difference Poisson-Boltzman Solver
MGMS - Molecular Surfaces Computation
8.) Quantum mechanical computation softwares
AMSOL - Semiempirical quantum chemistry program
Jaguar - ab initio software package
GAMESS
GAUSSIAN
MOPAC - Semiempirical quantum chemistry program
MOPAC 2000
QCPE - Quantum Chemistry Program Exchange
TURBOMOLE - Program Package for ab initio Electronic Structure Calculations
9.) Receptor-ligand interactions Softwares
DOCK - Docking of flexible ligands into protein target
FlexX - Automatic prediction of receptor-ligand interactions
FlexS - Automatic structural alignment of small organic molecules
TINKER - Software Tools for Molecular Design
10.) Scientific softwares
gnuplot - An Interactive Plotting Program
NLREG - Nonlinear Regression Analysis Program
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