Links to Molecular Structure Resources
Structure Databases
Reserach Collaboratory for Structural Bioinformatics
DNA Binding Proteins
Nucleic Acids
Collaborative Resource for Structural Genomics
Display and Graphics
PDB3D
PDB3D: Realtime 3D Molecule Renderer for the WWW running as interpreted
Java
PDB
to VRML converter
Proteins
in VRML Virtual Reality Modeling language
Rasmol
& Chime
RasMol is free software for looking at molecular structures.
Chime shows molecules inside a web page, freeware for Mac, PC and SGI
Nucleic Acids
- ICGEBnet DNA tools
- This server calculates various parameters from DNA sequences and
plots them. Three programs: plot.it, bend.it, curve.it.
- Curves
- Helical Analysis of Irregular Nucleic Acids, by R. Lavery and H. Sklenar
- mfold
- Interactive server to predict RNA folding, by M. Zuker
- Nucleic
Acids Database
- RNA
- the journal of the RNA Society
- Rnadraw
- RNA drawing and analysis tools, for MS Windows
- RNA
World
- the most comprehensive RNA site, at IMB Jena. Many links for programs,
structural and sequence databases.
- SCOP:
Nucleic Acids
- Structural Classification of Proteins classifies nucleic acids too.
Each entry can be viewed in VRML or RasMol.
Proteins
- Baylor
College of Medicine Search Launcher
- Starting point for sequence and pattern searches, alignments and secondary
structure predition
- Biotech
Validation Suite for Protein Structures
- just upload your coordinates to have your structure checked by PROCHECK,
SurVol, and WhatIf
- EMBL:the
PredictProtein server
- generate multiple sequence alignments, secondary structure, residue
solvent accessibility, transmembrane helices, topology for transmembrane
proteins, and fold recognition.
- ExPASy
- THE molecular biology server: Swiss Prot, Prosite, Enzyme, CD40Lbase,
and Seqence Analysis bibliographic reference database
- NOAMI
- NAOMI 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 Database
- Protein motions can be viewed in VRML or as a movie. Movies are either
CPK, stick, or ribbon and in stereo. Great site.
- Protein
Society
- The journal Protein Science here, also kinemages and registration for
the Protein Society meeting.
- PROWL - Skirball
- Databases 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 Group
- Protein Structure Analysis, Sequence Analysis, Structure Classification
(CATH)