Protein 3-D Structure Prediction Comparison

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information. - [Read more 3D-pssm]

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions. - [Read more BioInfo3D]

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization. - [Read more BSDD]

CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and - [Read more CaspR]

Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). - [Read more CATH]

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 JO - [Read more CE-MC]

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties. - [Read more ClusPro]

COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file - [Read more COLORADO-3D]

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank. - [Read more Combinatorial Extension of the Optimal Path]

The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regions for comparative modelling. - [Read more Consensus Server]

ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of - [Read more ConSeq]

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignmen - [Read more ConSurf]

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a prot - [Read more ElNemo]

FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT - [Read more FATCAT]

FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOC - [Read more FoldMiner and LOCK 2]

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures. - [Read more iMOT]

Program for displaying 3D structural information in a multiple sequence alignment. - [Read more JOY]

Homology or comparative modeling of 3D protein structures. - [Read more Modeller]

Excellent hands-on Swiss-PdbViewer/Deep View tutorial; a must-do before attempting to use Swiss-PdbViewer. - [Read more Molecular Modeling for Beginners]

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight - [Read more PDB2PQR Server]

PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites. - [Read more PDBSiteScan]

PepBuild is a tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format. - [Read more PepBuild]

Persistence of Vision Raytracer; use in conjunction with Swiss-PdbViewer to create graphics for presentation and publication. - [Read more POV-Ray]

ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. - [Read more ProteinDBS]

ProteMiner-SSM searches the PDB for proteins with similar tertiary substructures to one specified by the user. A filtering process is used to significantly speed up the analysis. - [Read more ProteMiner-SSM]

pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure. - [Read more pvSOAR]

The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is emplo - [Read more Robetta]

SA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment. - [Read more SA-Search]

SCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurall - [Read more SCit]

Structural Classification of Proteins - database created by a combination of manual inspection and automated methods. - [Read more SCOP]