NMR and Structural Biology Links on the Web compiled by Shauna Farr-Jones for Nature Structural Biology.
Editor's note:
Because this list was compiled in 1997 for the first NMR supplement for Nature Structural Biology, some of the links may no longer be valid.
BioMagResBankRepository for data from NMR spectroscopy on proteins, peptides, and
nucleic acidsCalculate
Chemical shifts of ProteinsUniversity of Sheffield, UK; Calculate proton chemical shifts, ring current shifts in proteins and second derivatives of ring current shifts to estimate temperature coefficients.Complex
Carbohydrate Research CenterInteractive carbohydrate spectral analysis server.Ensemble
AnalysisNMRCLUST-- Automated Approach For Clustering An Ensemble Of NMR-Derived Protein Structures Into Conformationally-Related Subfamilies. from Sutcliffe
group, University of LeicesterGAMMAGAMMA is a free interactive package designed to facilitate construction of programs that simulate magnetic resonance phenomena. by S. A. Smith
& T. Levante.Newera NMR tubesSolid State Simulation
and AnalysisChemical shift index, protein structure analysis, curve fitting and
many more free programs, from Dalhousie, Canada.VinceVince 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. Can also be used for nucleic acids.Web-Elements, periodic table, Sheffield UKExcellent interactive periodic table. Access to NMR information, as
well as other physical and chemical data.WilmadNMR tubes
Analysis of Relaxation
DataModelfree and curve fitting, from Arthur Palmer III, at Columbia Univ.CORMA/MARDIGRASComplete relaxation analysis, from Thomas James at UC San FranciscoMORASSDerives cross-relaxation rates and interproton distances, from D. Gorenstein at U. Texas Medical Branch
ANSIGAssignment of NMR Spectra by Interactive Graphics, by Per KraulisProntoPronto 3D2 can analyse multidimensional spectra as well
as display 3D structures. It is free from the Carlsberg Lab.SparkyUC San Francisco NMR display and Analysis Software. Manages resonance database and assists assignment. Now runs on x-windows. by T. Goddard and
D.G. Kneller.XEASYETH Automated Spectroscopy for X Window Systems
American Type Culture Collectionbugs, cells, vectors, hosts, fungi, and patent depository Baculoviruseukaryotic expression system to express proteins with post-translational modifications.Pichia pastorisPichia expression system for producing high levels of functionally
active recombinant protein. Uses methanol as a carbon source.
MidasPlus UCSF Molecular GraphicsUC San Francisco MidasPlus - Molecular Display and Simulation System
MOLMOLMOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special
emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95 and is freely available. by Reto KoradiMolscriptMolScript is a program for creating molecular graphics in the form
of PostScript plot files, by Per KraulisPDB3DPDB3D: Realtime 3D Molecule Renderer for the WWW running as interpreted JavaPDB to VRML converterProteins
in VRMLVirtual Reality Modeling languageRasmol & ChimeRasMol is free software for looking at molecular structures. Chime shows molecules inside a web page, freeware for Mac, PC and SGI
AMBERKollman, Case, & Pearlman, molecular dynamics and mechanics. DYANAby Guntert & Mumenthaler, structure calculation via torsion
angle dynamics.GROMOSvan Gunsteren Group. Dynamic Modelling of Molecular Systems.MSI/BIOSYMCommercial siteNetSci:Molecular Modeling ProgramsAn extensive list of molecular modeling programs, both academic and
commercial.Nilges group, EMBLX-plor refinement protocols and ARIAOxford MolecularCommercial siteX-plorAxel Brunger's research group. In addition to the X-plor manual and
information for downloading, this site has a cut and paste table of special charaters for netscape.
ICGEBnet DNA toolsThis server calculates various parameters from DNA sequences and plots them. Three programs: plot.it, bend.it, curve.it.CurvesHelical Analysis of Irregular Nucleic Acids, by R. Lavery and H. SklenarmfoldInteractive server to predict RNA folding, by M. Zucker Nucleic Acids DatabaseRNAthe journal of the RNA SocietyRnadrawRNA drawing and analysis tools, for MS WindowsRNA Worldthe most comprehensive RNA site, at IMB Jena. Many links for programs, structural and sequence databases.SCOP: Nucleic AcidsStructural Classification of Proteins classifies nucleic acids too.
Each entry can be viewed in VRML or RasMol.
Baylor College of Medicine Search LauncherStarting point for sequence and pattern searches, alignments and secondary structure predictionBiotech Validation Suite for Protein Structuresjust upload your coordinates to have your structure checked by PROCHECK, SurVol, and WhatIfEMBL:the PredictProtein servergenerate multiple sequence alignmnets, secondary structure, resifue
solvent accessibility, transmembrane helices, topology for transmembrane proteins, and fold recognition.ExPASyTHE molecular biology server: Swiss Prot, Prosite, Enzyme, CD40Lbase, and Seqence Analysis bibliographic reference databaseNAOMINAOMI is a computer program system for studying, manipulating and predicting features and properties of three-dimensional protein structures. It runs only on Silicon Graphics SGI compuer systems. by S. Brocklehurst. Employs fuzzy logic to define elements of structure, and other novel algorithms.Protein
Motions DatabaseProtein motions can be viewed in VRML or as a movie. Movies are either CPK, stick, or ribbon and in stereo. Great site.Protein SocietyThe journal Protein Science here, also kinemages and registration for the Protein Society meeting.PROWL - SkirballDatabases on peptides, nucleic acids and carbohydrates. Calculators
for molecular weights. Tending towards use for mass spectroscopy. Also and entry point for many web resources.Univ College London Biochemistry Biomolecular Structure GroupProtein Structure Analysis, Sequence Analysis, Structure Classification (CATH)
