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 to Go or NCBI.
PHYRE2 - 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. Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate. It also incorporates a new ab initio folding simulation called Poing to model regions of your proteins with no detectable homology. (Reference: Kelley LA et al. Nature Protocols 10: 845-858 (2015).
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, or Cn3D.
I-TASSER ONLINE - 3D models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations; function inslights are then derived by matching the predicted models with protein function databases. I-TASSER was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. (Reference: A. Roy et al. 2010. Nature Protocols 5: 725-738)
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).
PEP-FOLD 3 is a de novo approach aimed at predicting peptide structures from amino acid sequences. This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field. (Reference: Lamiable A, et al. Nucleic Acids Res. 2016; 44(W1): W449-54).
(PS)2: protein structure prediction server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain.(Reference: T-T. Huang et al. 2015. Nucl. Acids Res. 43 (W1): W338-W342).
BetaCavityWeb: computing molecular voids and channels with their mass properties. The output consists of three components: 1) the number of cavities, 2) the atoms contributing to the boundary of each cavity, and 3) the geometric property of each cavity. Computational statistics are also reported. The probe radius of zero corresponds to the cavities existing in the van der Waals molecules. If the probe radius is nonzero, the cavities are thoese existing in the Lee-Richards (solvent accessible) model. (Reference: J-K. Kim et al. 2015. Nucl. Acids Res. 43 (W1): W413-W418).
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.
RaptorX - consists of four major modules: single-template threading, alignment quality assessment, and multiple-template threading. (Reference: Källberg, M. et al. 2012. Nat Protoc. 7(8):1511-1522).
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 - 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. (Reference: S.S. Negi et al. 2007. Bioinformatics. 23: 3397-3399)
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).
PSIPRED Protein Sequence Analysis Workbench - includes PSIPRED v3.3 (Predict Secondary Structure); DISOPRED3 & DISOPRED2 (Disorder Prediction); pGenTHREADER (Profile Based Fold Recognition); MEMSAT3 & MEMSAT-SVM (Membrane Helix Prediction); BioSerf v2.0 (Automated Homology Modelling); DomPred (Protein Domain Prediction); FFPred 3 (Eukaryotic Function Prediction); GenTHREADER (Rapid Fold Recognition); MEMPACK (SVM Prediction of TM Topology and Helix Packing) pDomTHREADER (Fold Domain Recognition); and, DomSerf v2.0 (Automated Domain Modelling by Homology). (Reference: Buchan DWA et al. 2013. Nucl. Acids Res. 41 (W1): W340-W348).
MODELLER - comparative protein structure modelling by satisfaction od spacial constrains
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
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).
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)
SuperPose - is a protein superposition server. It calculates protein superpositions using a modified quaternion approach. From a superposition of two or more structures, SuperPose generates sequence alignments, structure alignments, PDB coordinates, RMSD statistics, Difference Distance Plots, and interactive images of the superimposed structures. The SuperPose web server supports the submission of either PDB-formatted files or PDB accession numbers. (Reference: Maiti, R. et al. 2004. Nucleic Acids Res. 32 (Web Server issue: W590-594).
3D-Match - Comparing 3D structures of two proteins (Softberry)
iPBA - is a tool for comparison of protein structures based on similarity in the local backbone conformation. It presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. (Reference: Gelly, J.C. et al. 2011. Nucleic Acids Res. 39(Web Server issue):W18-23).
MAPSCI Multiple Alignment of Protein Structures and Consensus Identification. The algorithm represents each protein as a sequence of triples of coordinates of the alpha-carbon atoms along the backbone. It then computes iteratively a sequence of transformation matrices (i.e., translations and rotations) to align the proteins in space and generate the consensus. The algorithm is a heuristic in that it computes an approximation to the optimal alignment that minimizes the sum of the pairwise distances between the consensus and the transformed protein. (Reference: Ilinkin, I. et al. 2010. BMC Bioinformatics. 11:71).
Rclick - this web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. It also recognizes conformational changes between structures. (References: Nguyen MN, & Verma C. 2015. Bioinformatics 31:966-968).
Presentation of data:
The NGL Viewer is a web application for the visualization of macromolecular structures. By fully adopting capabilities of modern web browsers, such as WebGL, for molecular graphics, the viewer can interactively display large molecular complexes and is also unaffected by the retirement of third-party plug-ins like Flash and Java Applets. Beautiful output. (Reference: A.S. Rose & P.W. Hildebrand. 2015. Nucl. Acids Res. 43 (W1): W576-W579).
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..
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).
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).
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. (Reference: Choi Y et al. 2012. PLoS One 7:e46688).
CUPSAT - Cologne University Protein Stability Analysis Tool - predicts changes in protein stability upon point mutations. The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site. Additionally, the prediction model can distinguish the amino acid environment using its solvent accessibility and secondary structure specificity. (Reference: Parthiban V, et al. (2006) Nucleic Acids Research, 34: W239-42.
Eris - is a protein stability prediction server. This server calculates the change of the protein stability induced by mutations (ΔΔG) utilizing the recently developed Medusa modeling suite. In our test study, the ΔΔG values of a large dataset (>500) were calculated and compared with the experimental data and significant correlations are found. The correlation coefficients vary from 0.5 to 0.8. Eris also allows refinement of the protein structure when high-resolution structures are not available. (Reference: Yin, F. et al. Nature Methods 4: 466-467; 2007)
AUTO-MUTE - AUTOmated server for predicting...functional consequences of amino acid MUTations in protEins - is a suite of programs measuring stability changes (ΔΔG, ΔΔGH2O, and ΔTm). (Reference: Masso M. & Vaisman I.I. (2010) Protein Eng. Des. Sel. 23: 683-687).
DUET - Protein Stability Change Upon Mutation - a web server for an integrated computational approach for studying missense mutations in proteins. DUET consolidates two complementary approaches (mCSM and SDM) in a consensus prediction, obtained by combining the results of the separate methods in an optimised predictor using Support Vector Machines (SVM). (Reference: D.E.V. Pires et al. 2015. Nucl. Acids Res. 42(1): W314-W319)
Pockets (active sites) in 3D structures of proteins:
metaPocket 2.0 - Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction (Reference: Zhang, Z. et al. 2011. Bioinformatics, 27: 2083-2088).
POCASA (POcket-CAvity Search Application) is an automatic program that implements the algorithm named Roll which can predict binding sites by detecting pockets and cavities of proteins of known 3D structure. (Reference: Yu, J. et al. 2010. Bioinformatics; 26: 46-52.)
Fpocket suite - three servers are available: (a) Fpocket: perform simple pocket detection; (b) MDpocket: track pockets in molecular dynamics; and, (c) Hpocket: view conserved pockets withing homologous proteins (Reference: Schmidtke P et al. 2009. Nucleic Acids Res.10:168).
Mutation and crystallization:
SERp Server - Surface Entropy Reduction prediction (SERp) is an exploratory tool to aid identification of sites that are most suitable for mutation designed to enhance crystallizability by a Surface Entropy Reduction approach. (Reference: Goldschmidt L et al. 2007. Protein Sci. 16:1569-76).
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).