PROTEIN TERTIARY STRUCTURE Sites are offered for calculating and displaying the 3-D structure of oligosaccharides and proteins. With the two protein  analysis sites the query protein is compared with existing protein structures as revealed through homology analysis.

Background: "Principles of Protein Structure, Comparative Protein Modelling and Visualization" by N. Guex & M.C.  Peitsch (GlaxoWellcome, Switzerland) is here. To obtain PDB coordinates for a protein of your interest, go to the Protein Data Bank or Molecules R Us or NCBI.

3D-PSSM - (Imperial Cancer Research Fund Fold Recognition Server) A Fast, Web-based Method for protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure and solvation potential information.  See also here.

Its successor is PHYRE - Protein Homology/analogY Recognition Engine - this is my favourite site for the prediction of the 3D structure of proteins.  In each case I have used this site it has provide me with a model.

CPHModels (Center for Biological Sequence Analysis, Technical University of Denmark) - currently consists of the following tools: Sowhat: A neural network based method to predict contacts between C-alpha atoms from the amino acid sequence. RedHom: A tool to find a subset with low sequence similarity in a database. Databases: Subsets of the Brookhaven Protein Data Bank (PDB) database with low sequence similarity produced using the RedHom tool.
SWISS-MODEL - (Glaxo-Wellcome Experimental Research, Switzerland)  An automated comparative protein modelling server. Choose "First Approach mode". N.B. results come by E-mail and require a viewer such as DeepView - Swiss-PdbViewer, Rasmol, Cn3D v3.0 or WebMol Java PDB Viewer to visualize.  
LIBELLULA (Protein Design Group. CNB-CSIC, Spain) -  a neural network approach to evaluate fold recognition results.  Results by email. Save and view with Rasmol etc.
LOOPP (Learning, Observing and Outputting Protein Patterns) (Computational Biology Service Unit, Cornell Univ., U.S.A.) -  is a fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure. The signals we are using include straightforward sequence alignment, sequence profile, threading, secondary structure and exposed surface area prediction. Excellent.

ESyPred3D - this automated homology modeling program derives benefit from a new alignment strategy using neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER. (Reference: C. Lambert et al. 2002. Bioinformatics 18: 1250-1256).

AS2TS system - offers a variety of resources for protein structural analysis using the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, the AL2TS service translates given sequence–structure alignment data into the standard PDB coordinates (Reference: A. Zemla et al. 2005. Nucl. Acids Res. 33: W111-W115).

3D-JIGSAW (Biomolecular Modelling Laboratory, Cancer Research UK, England) - homology modelling. Save email results as *.pdb and view with Rasmol etc.
  WHAT IF Web Interface (Centre for Molecular and Biomolecular Informatics, University of Nijmegen, Holland) offers one a large number of tools for examining PDB files.

Protein Peeling: an approach for splitting a 3D protein structure into compact fragments -  a method to identify small compact units (protein units (PU)) that compose protein three-dimensional structures. (Reference:  J.-C. Gelly et al. 2006. Bioinformatics 22: 129-133)

 InterProSurf (Reference: S.S. Negi et al. 2007. Bioinformatics. 23: 3397-3399) - predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities.

 ProtSkin converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP, MOLMOL or PyMOL. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys). (Reference: Deprez, C. et al. 2005. J. Mol. Biol. 346: 1047-1057)

Structures derived from NMR coordinates

 GeNMR (GEnerate NMR structure) - generates 3D protein structures using NOE-derived distance restraints and NMR chemical shifts. (Reference: M. Berjanskii et al. 2009. Nucl. Acids Res. 37(Web Server issue):W670-W677)

Once you have a structure you may want to superimpose it on other molecules. To obtain PDB accession codes for a protein of your interest, go to the Protein Data Bank or Molecules R Us. One site is available:

FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison. It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure. (Reference: Y.Ye & A. Godzik. (2003) Bioinformatics 19: suppl. 2. ii246-ii255).

 Dali Server - this is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Once you have a match you can use the pairwise DaliLite server to compare them.

 Search for Similar Protein Structures by FATCAT  - either upload local PDB files or simply provide PDB codes. For close homologs go here (Reference: Y. Ye & A. Godzik. 2003. Bioinformatics 19(Suppl 2):II246-II255)

Presentation of data:

AISMIG (An Interactive Server-side Molecule Image Generator) - visualization of molecules on the Internet normally is usually done using Java Applets like jmol or webmol, Plugins like Chime or external helper applications like Rasmol which only  generate low resolution pictures i.e. are not suitable for publication purposes.  This program produces incredible graphics (Reference: A. Bohne-Lang et al. 2005. Nucl. Acids Res. 33: W705- W709)

CEP: a conformational epitope prediction server - provides a web interface to conformational epitope prediction. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. (Reference: U. Kulkarni-Kale et al. 2005.  Nucl. Acids Res. 33: W168-W171). The following is an example of an epitope (space-filled) mapped onto the partial surface (stick) of lysozyme:

PDB2MultiGIF (Central Spectroscopy Department - Molecular Modeling, Deutsches Krebsforschungszentrum, Germany) - if you want to present your model on a webpage in a similar manner to the three pictures on the entry page use this program. It takes the 3D structure (PDB file) and generates an animated image which can be displayed using any browser. There is considerable choice on the image size, number of frames and direction of rotation.

Protein Picture Generator - generates static or animated pictures from a protein structure file (PDB). Offers a huge number of controls on the presentation format. (Reference: C. Binisti et al. 2005. Nucl. Acids Res. 33: W320- W323).

MovieMaker -  a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating 1) simple rotation 2) morphing between two end conformers 3) short-scale, picosecond vibrations; 4) ligand docking; 5) protein oligomerization; 6) mid-scale nanosecond (ensemble) motions; and 7) protein folding/unfolding.  MovieMaker is not a molecular dynamics server and does not perform MD calculations. (Reference: R. Maiti et al. 2005. Nucl. Acids Res. 33: W358-W362)

COMBOSA3D - Coloring Of Molecules Based On Sequence Alignment (Paul Stoddard) - accepts a group of pre-aligned sequences in FASTA format (one of the sequences must have a solved three-dimensional structure), and it uses the alignment information to highlight conserved residues on the molecule. Three-dimensional structures are shown using a Chime plugin or one may use RasMol to view and color a molecule..

Data mining:

ProFunc: a server for predicting protein function from 3D structure - this program takes PDB files and carries out an awesome array of analyses including scans against PDB and motif databases, determination of surface morphology and conserved residues, and potential ligand-binding sites. (Reference: R. A. Laskowski et al. 2005. Nucl. Acids Res. 33: W89-W93).
Pocket-Finder (Bioinformatics, University of Leeds, Great Britain) - is a pocket detection algorithm which works by scanning a probe radius 1.6 angstoms along all gridlines of a grid resolution 0.9 angstroms surrounding the protein. The probe also scans cubic diagonals. Grid points are defined to be part of a site when the probe is within range of protein atoms followed by free space followed by protein atoms. Since the protein is scanned in seven directions, each grid point can be defined to be part of a site up to seven times. Grid points are only retained if they are defined to be part of a site at least five times.

Q-SiteFinder (Bioinformatics, University of Leeds, Great Britain) - is a new method of ligand binding site prediction. It works by binding hydrophobic (CH3) probes to the protein, and finding clusters of probes with the most favorable binding energy. These clusters are placed in rank order of the likelihood of being a binding site according to the sum total binding energies for each cluster.

P-cats - Prediction of CATalytic residueS in proteins - predicts the catalytic residues in proteins from the atomic coordinates. (Reference: K. Kinoshita & M. Ota. 2005. Bioinformatics 2005 21: 3570-3571)

Predict Function from Structure:

ProFunc - is been developed to help identify the likely biochemical function of a protein from its three-dimensional structure using a variety of sequence- and structure-based methods (Reference: Laskowski R.A. et al. 2005. Nucleic Acids Res.33, W89-W93).

Metasite:

 Scratch Protein Predictor - (Institute for Genomics and Bioinformatics, University California, Irvine) - programs include: ACCpro: the relative solvent accessibility of protein residues; CMAPpro: Prediction of amino acid contact maps; COBEpro: Prediction of continuous B-cell epitopes; CONpro: predicts whether the number of contacts of each residue in a protein is above or below the average for that residue; DIpro: Prediction of disulphide bridges; DISpro: Prediction of disordered regions; DOMpro: Prediction of domains; SSpro: Prediction of protein secondary structure; SVMcon: Prediction of amino acid contact maps using Support Vector Machines; and, 3Dpro: Prediction of protein tertiary structure (Ab Initio).