Links

Databases

NCBI  - National Center for Biotechnology Information

EBI  - European Bioinformatics Institute

TIGR  - The Institute for Genomic Research

Swiss-Prot  - Protein Knowledgebase

PDB  - Protein Data Bank                  

PDBsum  

BMRB  - Biological Magnetic Resonance Data Bank

PepcDB  - Protein Expression Purification and Crystallization Database

Database of Macromolecular Movements  - with Associated Tools for Flexibility and Geometric Analysis

CMR  - Comprehensive Microbial Resource

Colibri  - Escherichia coli Genome Web Server

Subtilist  - Bacillus subtilis Genome Web Server

SGD  - Saccharomyces Genome Database

BioCyc - a collection of 371 Pathway/Genome Databases

TAIR - The Arabidopsis Information Resource

Protein Structure Tools

CATH  - Protein Structure Classification                                            

Cathedral Server  - Structure and Sequence Comparison

SCOP  - Structural Classification of Proteins

DALI  - Comparing 3D Protein Structures against those in PDB              

DaLiLite  - Pairwise Comparison of Protein Structures

SWISS-MODEL  - An Automated Comparative Protein Modelling Server

Meta-Server at CBS  - 3D Structure Modelling

ModPipe  - An Automated Software Pipeline for Protein Structure Modelling

PROCHECK  - Check the Stereochemical Quality of a Protein Structure

WHAT IF  - a Versatile Molecular Modelling Package                        

WHAT IF Server

Sequence Analysis Tools

Blast at NCBI       

WU-BLAST at EBI    

ExPASy  - Expert Protein Analysis System

SMART  - Simple Modular Architecture Research Tool

STRING - Search Tool for the Retrieval of Interacting Proteins

PredictProtein  - Sequence Analysis and Prediction of Structure and Function

Translate  - Translate a Nucleotide Sequence to a Protein Sequence   

pI/Mw  - Computation of the Theoretical pI and Mw

ProtParam  - Computation of Physical and Chemical Parameters for a Protein

DisProt  - Predictor of Protein Disorder

TMHMM  - Prediction of transmembrane helices in proteins (CBS; Denmark)           

DAS  - Prediction of transmembrane regions in prokaryotes (Stockholm University)

ClustalW  - Multiple Sequence Alignment

ESPript  - Generate a PostScript Output from Aligned Sequences

Journals

Biochemistry

BBRC

Cell

EMBO J

JACS

J Bacteriol

JBC

Molecular Cell

Nature

Nature Structural and Molecular Biology

PLOS Biology

PNAS

Science

Software

NMRPipe  - a Multidimensional Spectral Processing System Based on UNIX Pipes

TALOS  - Torsion Angle Likelihood Obtained from Shift and sequence similarity

NMRView  - A Program for Visualization and Analysis of Processed NMR Data

CARA  - Computer Aided Resonance Assignment

MARS  - Robust Automatic Backbone Assignment

CYANA  - Combined Assignment and Dynamics Algorithm for NMR Applications

AMBER  - Assisted Model Building with Energy Refinement

SUPPOSE  - Multiple Superposition of Protein Structures

MOLMOL  - Analysis and Display of Molecules

ModelFree  - A Program for Optimizing "Lipari-Szabo Model Free" Parameters to Heteronuclear Relaxation Data

CPMGFit  - Programs for Non-linear Least Squares Fitting of CPMG Relaxation Dispersion Curves

TENSOR  - Determination of the Rotational Diffusion Tensor

MODULE  - Rigid-Body Modeling of Multi-Domain Macromolecules using Residual Dipolar Couplings

PALES  - Prediction of Alignment Tensor from Protein Structure

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