Application Index

This is a collection of tools for biomolecular structure determination, refinement and analysis from crystallographic or NMR data.

ANSIG is a program for viewing and assigning 2D, 3D and 4D NMR spectra of biological macromolecules. It is written in Fortran 77 and used in Silicon Graphics machines. The input data of the program are frequency-domain spectrum matrices, together with the sequence of the protein. All processing of the spectral matrices must have been done before ANSIG can be used to view the spectra. It is available for free for academic institutions.
View Application Entry for ANSIG

AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was initially developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands. It is currently maintained and expanded by Jurgen Doreleijers at the BioMagResBank, University of Wisconsin-Madison, USA.
View Application Entry for AQUA

A system for the refinement of protein structures via automatic updating and re-building of the model and solvent structure
View Application Entry for ARP/wARP

The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. The programs are distributed in source form, so they can be studied (do not look too closely!), modified and fixed by recipients, in contrast to most commercial software.
View Application Entry for CCP4

CNS is a system for structure determination from crystallographic or NMR data. It is available for free and is supported on Unix or Windows NT machines.
View Application Entry for CNS

CNX(Crystallography and NMR Explorer) is based on the widely used programs X-PLOR and CNS. CNX extends the capabilities and offers functionality that can significantly increase the speed of the structure solution process. This free program integrates X-ray diffraction and NMR spectroscopic data with molecular mechanics, dynamics, and energy minimization to aid in the solution of three-dimensional molecular structures. In addition, CNX offers state of the art algorithms such as maximum likelihood refinement for X-ray refinement and residual dipolar coupling restraints for NMR structure determination. All of these protocols can be easily setup and customized through an HTML-based interface that provides template protocols. In addition, CNX uses several supported force fields including the Engh-Huber and CHARMm force fields. CNX is supported on SGI and LINUX platforms.
View Application Entry for CNX (Crystallography and NMR Explorer)

CYANA (Combined assignment and dYnamics Algorithm for NMR Applications) is a program for the structure calculation of biological macromolecules on the basis of conformational constraints from NMR. CYANA features the full functionality of its predecessor program, DYANA, and many new options, including the CANDID (by Peter Güntert and Torsten Herrmann) method for automated assignment of NOESY spectra.
View Application Entry for CYANA (Combined assignment and dYnamics Algorithm for NMR Applications)

FANTOM is a program which can calculate low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments.
View Application Entry for FANTOM (Fast Newton-Raphson Torsion Angle Minimizer)

FELIX is a commercial program used for data processing, spectral visualization and analysis for all types of high resolution, one- dimensional to four dimensional, homonuclear and heteronuclear NMR data. It is supported on Silicon Graphics or IBM RS/6000 or Sun(Solaris OS) workstations.
View Application Entry for FELIX

GAMMA (General Approach To Magnetic Resonance Mathematical Analysis) is a C++ library written for simulation of Magnetic Resonance experiments. Its purpose is to provide a simple and intuitive means with which users may construct simulation programs to suit their individual needs.
View Application Entry for GAMMA (General Approach To Magnetic Resonance Mathematical Analysis)

GARANT (General Algorithm for Resonance AssignmeNT) is an algorithm for automatic resonance assignment using as input the primary structure of a protein and lists with observed cross peaks from various spectra; knowledge about magnetization transfer pathways in the NMR experiments used is read from a library. The basic concept of GARANT is the matching of observed cross peaks to expected cross peaks derived from the sequence and the magnetization transfer pathways. GARANT is available free-of-charge to all users who agree with the copyright and legal information.
View Application Entry for GARANT (General Algorithm for Resonance AssignmeNT)

Gifa is a computer program designed for the processing, the visualization and the analysis of 1D, 2D, and 3D NMR data-set. Gifa as an NMR processing program includes all the standard (and not so standard) processing and display methods. It includes many powerful signal processing methods such as Maximum Entropy, Linear Prediction, automatic Phasing, line fiting, base line correction...etc. Sophisticated graphic interaction is possible (1D, 2D and 3D on screen, superposition of 1D and 2D spectra, fully interactive AND programmable GUI).
View Application Entry for Gifa

The HKL suite is a package of programs intended for the analysis of X-ray diffraction data collected from single crystals. It consists of three parts: XdisplayF for visualization of the diffraction pattern, Denzo for data reduction and integration, and Scalepack for merging and scaling of the intensities obtained by Denzo or other programs.
View Application Entry for HKL

MAIN is an interactivelly driven computer program dealing with computational parts of macromolecular crystallography. It provides visualisation and interactive modeling of molecular structures, density modifications (solvent flattening and fliping, envelopes manipulation, averaging), crystallographic refinement (real space and reciprocal space target) and structure analysis.
View Application Entry for MAIN

NMRView is a free program for the visualization and analysis of NMR data. Binaries are available for Solaris, Irix, Linux and Java 1.3-enabled platforms.
View Application Entry for NMRView

A program system for diffraction data analysis, MIR phase determination and molecular replacement calculations
View Application Entry for PROTEIN

RAVE is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging. It also contains tools for the detection of secondary structure elements in macromolecular electron-density maps. RAVE is available for SGI and DEC ALPHA computers. In addition to the RAVE programs, you need several CCP4 programs (SFALL, RSTATS and FFT; these are available from CCP4, Daresbury) and O (for displaying maps and providing spacegroup and other operators). The package includes an averaging tutorial.
View Application Entry for RAVE

SHARP is a computer program for macromolecular crystallography. It operates on reduced, merged and scaled data from SIR(AS), MIR(AS) and MAD experiments, refines the heavy-atom model, helps detect minor or disordered sites using likelihood-based residual maps, and calculates phase probability distributions for all reflexions in the dataset.
View Application Entry for SHARP (Statistical Heavy- Atom Refinement and Phasing)

SHELX is a set of programs for crystal structure determination from single-crystal diffraction data. It is available on Unix or Windows 95/98/NT/2000 machines and is freely available for academic users.
View Application Entry for SHELX

SIMPSON is a computer program for fast and accurate numerical simulation of solid-state NMR experiments. The program is designed to emulate NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, rf irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. It features multi-pulse 1D/2D experiments on large spin-systems with input-files implemented using a simple scripting language.
View Application Entry for SIMPSON

SnB is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. This program has been used in a routine fashion to solve difficult structures, containing as many as 1000 unique non-H atoms, that could not be solved by traditional reciprocal-space routines based on the tangent formula alone. Recently, SnB has also been used to determine the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 70 Se sites.
View Application Entry for SnB

SOLVE is a program that can carry out all the steps of macromolecular structure determination from scaling data to calculation of an electron density map, automatically. SOLVE does everything crystallographers do to solve an MIR or MAD structure, but automatically. It scales data, solves Patterson functions, calculates difference.
View Application Entry for SOLVE

Sparky is a free graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. It is available on SGI, SUN, DEC Alpha and Linux platforms.
View Application Entry for Sparky

TNT is a program package which is used to refine models of macromolecules. It is free for non-commercial research organizations. It has been tested on Compaq Alpha running either VMS or Unix, SGI systems running Irix, Pentium systems running Linux, and Sun systems running Solaris.
View Application Entry for TNT

Xsight is a commercial integrated system with a graphical user interface covering all aspects of protein crystal structure determination.
View Application Entry for Xsight

XtalView is a crystallographic software package for fitting electron density maps and solving structures by MIR and MAD. It uses an X-windows interface on a number of UNIX platforms (SGI, SUN, DEC and LINUX).
View Application Entry for XtalView