Application Index

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

UNIO enables you to perform automated NMR data analysis for protein 3D structure determination. UNIO NMR data analysis interconnects the MATCH algorithm for backbone assignment (1), the ASCAN algorithm for side-chain assignment (2) and the CANDID algorithm for NOE assignment (3). The ATNOS algorithm for robust signal identification in NMR spectra is employed to grant each of the three expert-systems direct access to the raw NMR data (4), thus enabling integrated and consistent data evaluation. The UNIO data analysis protocol requires only a minimal set of 3-6 NMR spectra, namely APSY and NOESY, and features high computational efficiency. The experience gained so far shows that the UNIO approach leads to objective and consistent NMR data interpretation (see UNIO structures).
View Application Entry for UNIO

CNX(Crystallography and NMR Explorer) is a program that integrates X-ray diffraction and NMR data with molecular dynamics to aid in the solution of three-dimensional molecular structures. It is based on the widely used programs X-PLOR and CNS. CNX is available for IBM, SGI and LINUX platforms.
View Application Entry for CNX (Crystallography and NMR Explorer)

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)

It is a tool to create diagrams of pulse sequences directly from Bruker AVANCE series pulse programs. Clipper is implemented in awk and creates a postcript file as output. Thus installation is trivial, clipper is very portable, and hardcopy output is guaranteed to be the same as you see on screen (in a postscript viewer). It was developed on SGI machines running IRIX, but has also been used less extensively under LINUX
View Application Entry for Clipper (Compact and LIteral Pulse ProgrammE Representation)

NMRCLUST is an Automated software for clustering an ensemble of NMR-Derived protein structures into conformationally-related subfamilies.
View Application Entry for NMRCLUST

Rowland NMR Toolkit is a suite of programs for processing multi-dimensional NMR data. In addition to providing support for conventional, DFT-based spectrum analysis, a set of ancillary tools provide support for modern methods of spectrum analysis, including linear prediction and maximum entropy reconstruction. The Toolkit runs on Unix workstations, and the graphical tools use X-Windows and PostScript. The Toolkit is capable of processing NMR data from most sources.
View Application Entry for Rowland NMR Toolkit

PROCHECK-NMR is a suite of programs that have been derived from the PROCHECK programs to analyse ensembles of protein structures solved by NMR.
View Application Entry for PROCHECK-NMR

Vince (VIsualization of Nuclear ConnEctivity) is a computer program for generating graphs summarizing nuclear Overhauser effects (NOEs) observed in proteins, in a form that is commonly used for publication. In addition, Vince can display secondary structure assignments, calculate and display chemical shift indices, or display other user-supplied data.
View Application Entry for Vince (VIsualization of Nuclear ConnEctivity)

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 Windows workstations.
View Application Entry for FELIX

CNS (Crystallography & NMR System) is a software suite for structure determination from crystallographic or NMR data. It is available for free and is supported on Unix, Linux and Windows NT machines.
View Application Entry for CNS (Crystallography & NMR System)

FANTOM is a program that calculates low-energy conformations of proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments. It is available for Unix platforms.
View Application Entry for FANTOM (Fast Newton-Raphson Torsion Angle Minimizer)

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. It is available for Unix and Linux platforms.
View Application Entry for CYANA (Combined assignment and dYnamics Algorithm for NMR Applications)

ARP/wARP is a software suite for improvement and objective interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models. It is used as a module within the CCP4 interface. The program is freely available to academic users provided the applications are properly cited.
View Application Entry for ARP/wARP

AQUA is a suite of programs for analyzing the quality of biomolecular structures that were determined via NMR spectroscopy. Output from AQUA can be read and visualized by PROCHECK-NMR, a program in the PROCHECK suite for assessing the stereochemical quality of protein structures. The AQUA suite is freely available for LINUX and Unix platforms and as a Web server.
View Application Entry for AQUA

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, modified and fixed by recipients. Fortran and C compilers are required to build the suite. It is available without cost to academic institutions but a charge is made to commercial users.
View Application Entry for CCP4

SwaN-MR is a free and comprehensive application to process and analyze all NMR spectra. It is the only reasonable solution for a Macintosh, and it is not available for other computers. The outstanding speed is noteworthy.
View Application Entry for SwaN-MR

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

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)

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

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.
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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

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.
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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

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

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

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.
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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.
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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.
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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

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