pET vectors - Novagen pET vector table
DNA/RNA Sequence Editor - Edit DNA and RNA sequence
Double Digestion Finder - Use this tool to select reaction conditions amenable to any two NEB restriction enzymes
Tm Calculator - Recommended when using Finnzymes' DyNAzyme, Phire and Phusion DNA Polymerases and DyNAmo qPCR Kits
DNA -> protein conversion - Convert DNA sequence to protein
Restriction analysis - Online restriction endonuclease site search tool
MultiBac - MultiBac information at ETH Zurich
Ensembl - Automatic annotation on selected eukaryotic genomes
Citric Buffer Calculator
- A JavaScript that calculates the amount of citric acid and sodium citrate necessary to achieve a buffer at a given pH and buffer strength
pI/Mw calculator - Calculate isoelectric point and molecular weight of proteins
ProtParam - Calculate various physical and chemical parameters for a given protein
GlobPlot2 - Domain linker prediction at RIKEN (graphic display is very clear)
SMART - Simple Modular Architecture Research Tool. To identify conserved domains/domain architectures, with particular emphasis on mobile eukaryotic domains
Prosite - Scan protein for conserved domains (seems good)
COILS - A program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score
DLP - Intrinsic Protein Disorder, Domain & Globularity Prediction (trust the 1st choice, but conservatively)
PSIPRED - Protein secondary structure prediction with visually attracting graphic output
META-PP - Submit one sequence to MULTIPLE servers for secondary structure prediction
Multi-alignment - Protein multiple sequence alignment with hierarchical clustering
ClustalW2 - Biologically meaningful multiple sequence alignments of divergent sequences, with evolutionary relationships available
Peptide cutter - Predicts potential protease cleavage sites on a given polypeptide
Recombinant Protein Solubility Prediction - Predict the solubility of recombinant proteins in Escherichia coli
GCUA - Graphical Codon Usage Analyser: display codon bias in different organisms in a graphical manner
Protein Colourer - Tool for coloring your amino acid sequence
ExPASy - ExPASy Proteomics tools
Reciprocal cell/Vm calculator - Calculate reciprocal cell and Matthews Coefficient
Space group tables - A hypertext book of crystallographic space group
diagrams and tables
Spacegroup Frequencies - Appearing frequencies of the 65 chiral spacegroup based on all PDB holdings up to 1 Feb, 2000
Euler & Matrix - rotation conversion
The DALI server - A network service for comparing protein structures in 3D
SWISS-MODEL - An Automated Comparative Protein Modelling Server
MUSTER (MUlti-Sources ThreadER) - Identify the template structures from the PDB library and provide models built by MODELLER (and top 5 template proteins plus the query-template alignments)
I-TASSER - An Internet service for protein structure and function predictions
ModWeb - A server for comparative protein structure modeling
Sawaya's homepage - A site with useful crystallographic topics
Kevin Cowtan's homepage - A site with interesting crystallographic topics
Chirgadze's homepage - A site describing crystallization and more
GXRCC - Georgia X-ray Crystallography Center
Some homemade operating tips - Posted on our in-house X-ray lab website
Jigsaw puzzles online - Just for fun
Energy converter - a handy conversion calculator for some common energy, wavelength and frequency terms
X-ray Anomalous Scattering - web-based absorption edge reference, etc.
BRUTEPTF - 6D searches to fit models to a phased map with very high root-mean-square deviation (up to 3.0 A and even higher in some cases)
Strategy
- A Program for the Determination of the Optimal Starting Spindle Angle in X-Ray Crystallography Data-Collection
HKL - Data processing and analysis
Scalepack - Alphabetical Scalepack Keyword Documentation
Solve - Automated structure solution for MIR and MAD
CNS v1.2
- For 3D structural determination of biomacromoleculs by X-ray or NMR
PHENIX - Python-based Hierarchical ENvironment for Integrated Xtallography
Phaser - A program for phasing macromolecular crystal structures with maximum likelihood methods (convenient for MR)
SHARP - sbgrid Sharp server
CCP4 - CCP4 v6.0.2 Program Documentation
USF - Uppsala Software Factory: manuals for Gerard's programs and links to other useful O or O-related information, programs and resources
GRASP - A molecular visualization program for the display of the surfaces of molecules and their electrostatic properties
Pymol - Visualizing structure and high-quality figure generation
RASMOL
- Good for fast viewing biological structures
Molscript
- High-quality renderings of known 3D structures
O - Manual for O version 5.10
Dock
- For computationally docking a ligand to a receptor
Unix/Linux- A brief overview of each of the Unix / Linux commands
Sparky
- Analysis of 2D and 3D NMR data
