BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.
The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.
The Biomolecule Stretching Data provides information about mechanostability of proteins. Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. Information on the possible types of the mechanical clamps (the motifs which are responsible for a protein's resistance to stretching) are also given.
A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.
Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.
DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
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