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3-D Structure Analysis
- Structure Annotation Tools
- Structural Analysis
- Domain Prediction, Globularity and Assembly Analysis
- Hinge & Flexibility
- Surface & Cavity Analysis
- Binding Pocket and Binding Site Prediction
- Ligand Interaction
- Sites & Motifs
- Interface Analysis
- Contact Maps
- Solvent Accessibility
- Functional & Conserved Residues
- Effects of Mutations
- Disulphide Bonds
- Metal Bindind Sites
Structure Annotation Tools
SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be coloured according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol.
ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences.
SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.
Structural Analysis
The Dali server is a network service for comparing protein structures in 3D. Access also to related tools: SRS search for FSSP (families of structurally similar proteins); search for DSSP; search for HSSP, (homology-derived structures of proteins), a derived database merging structural (2-D and 3-D) and sequence information (1-D).
PDBeMotif is an extremely fast and powerful search tool that facilitates exploration of the Protein Data Bank (PDB) by combining protein sequence, chemical structure and 3D data in a single search. Currently it is the only tool that offers this kind of integration at this speed. PDBeMotif can be used to examine the characteristics of the binding sites of single proteins or classes of proteins such as Kinases and the conserved structural features of their immediate environments either within the same specie or across different species.
The WHAT IF Web Interface proposes a varied set of analyses on protein structure.
The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods (see below) to try to provide clues as the the protein's likely or possible function. Often, where one method fails to provide any functional insight another may be more helpful.
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions;
PBE server 2.0 aims to provide a platform for protein structure
The ConSurf server is a useful and user-friendly tool that enables the identification of functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure, based on the phylogenetic relations between its close sequence homologues.
StrucToolsn is a set of tools intended to provide a convenient web interface to simple, commonly used structural biology calculations with PDB files.
STING Millennium is a web based suite of programs that starts with the visualization of a molecular structure and leads the user through a series of operations resulting in an extensive structural analysis of the molecule
firestar server: predicting functional residues from structural templates and alignment reliability
Evaluating the salt brIdges in proteins.
This program allows to analyse contacts between two chains or within one chain in a given PDB file.
HORI - Higher Order Residue Interactions, is a web server to compute higher order interactions (pairwise interaction, triplet interactions and quadruple interactions) in a protein structure.
MolTalk is a computational environment for doing Structural Bioinformatics. At the base of i.Moltalk
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
Web resource for the identification of sequence-structure links. The resource consists of an exhaustive collection of annotated links between the Swiss-Prot + TrEMBL sequence database entries and the PDB and SCOP structure database entries.
Domain Prediction, Globularity and Assembly Analysis
pDomain resource is centered around defining structural domains from 3D coordinates. This resource brings together current state-of-the-art algorithmic methods for partitioning proteins into domains.
Search for Conserved Domains within a protein sequence.
Dompred is a server designed to predict putative protein domains and their boundaries for a given protein sequence. The server uses several methods, from identifying obvious similarities to Pfam-A domain sequences to predicting domains using DomSSEA in cases where sequence searching has yielded no results.
The approach 'Protein Peeling' aims at cutting the 3D protein structure into a limited set of 'Protein Units'. A more precise definition of protein unit is a compact sub-region of the 3D structure corresponding to one sequence fragment.
DOMpro is a web server to predict protein domain boundaries using 1D-Recursive Neural Networks and statistical methods.
DIAL is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
PURE is a bioinformatics protocol to identify putative domains in the Unassigned Regions.
Domain 3D is a method developed by Willie Taylor to identify globular domains in protein structure.
DHcL (Domain Hierarchy and closed Loops)is a server for the analysis of basic structural units of a protein. The server calculates domain structures at different levels of energy hierarchy and elements of the loop-n-lock structure, closed loops and van derWaals locks.
Hinge & Flexibility
DynDom is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available.
An Algorithm For Protein Hinge Prediction Using Elastic Network Models
Analysis of Flexibility in Biomolecules and Networks.
Analysis of Flexibility in Biomolecules and Networks.
TLS Motion Determination (TLSMD) analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.
Surface & Cavity Analysis
CAVER is a software tool for analysis and visualisation of channels (tunnels) in protein structures. Channels are void pathways leading from a cavity buried in a protein core to the surrounding solvent. Studying of these pathways is highly important for drug design and molecular enzymology.
3D-SURFER is web-based software for protein surface comparison and analysis. The server integrates various repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons. It takes less than a second to perform an exhaustive comparison between a single protein surface to all protein structures in the current PDB. Conveniently, the web interface also renders animated protein rotations, displays CATH codes [Orengo CA, Structure, 1997], and structure alignment calculations using the Combinatorial Extension (CE) algorithm [Shindyalov IN and Bourne PE, Protein Eng, 1998]
Accurate identification of channels in macromolecules.
SURF's_UP! is a web tool for analysis of functional relationships in protein families as inferred from protein surface maps comparison. It addresses a situation where only few members of the large homologous family are characterized by experiment and function of others are unknown, either in a general sense or in details (e.g. hydrolase with unknown specificity).
Molecular surface of proteins with the electrostatic potential is a representation of protein three dimensional structures, which often gives some clues to infer the function of proteins. eF-surf is a web server to calculate the molecular surface of the up-loaded file with PDB format.
Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities. castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions;
HotPatch finds unusual patches on the surface of proteins, and computes just how unusual they are (patch rareness), and how likely each patch is to be of functional importance (functional confidence (FC).) The statistical analysis is done by comparing your protein's surface against the surfaces of a large set of proteins whose functional sites are known.
Binding Pocket and Binding Site Prediction
IBIS is the NCBI Inferred Biomolecular Interactions Server. For a given protein sequence or structure query, IBIS reports physical interactions observed in experimentally-determined structures for this protein. IBIS also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query.
Pocket-Finder is a pocket detection algorithm based on Ligsite written by Hendlich et al (1997). Pocket-Finder works by scanning a probe radius 1.6 angstoms along all gridlines of a grid resolution 0.9 angstroms surrounding the protein.
FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
LIGSITE is a web server for the automatic identification of pockets on protein surface using the Connolly surface and the degree of conservation!
PocketPicker - Binding Site Prediction
metaPocket is a meta server to identify pockets on protein surface to predict ligand-binding sites!
castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
3DLigandSite is an automated method for the prediction of ligand binding sites.
The MEDock (Maximum-Entropy based Docking) web server is aimed at providing an efficient utility for prediction of ligand binding site.
Q-SiteFinder 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 favourable 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.
Metal ion binding sites, affinities, and specificities from structure
Protein binding site prediction with an empirical scoring function.
The aim of this server is to predict MHC Class-II binding regions in an antigen sequence, using quantitative matrices.
Ligand Interaction
STITCH is a resource to explore known and predicted interactions of chemicals and proteins.
Ligand-Protein Contacts & Contacts of Structural Units.
Program for automatically plotting protein-ligand interactions.
Sites & Motifs
The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme.
SuMo allows you to screen the Protein Data Bank (PDB) for finding ligand binding sites matching your protein structure or inversely, for finding protein structures matching a given site in your protein. This method is neither based on aminoacid sequence nor on fold comparisons.
All structures are reduced to matrices that contain just enough information to define a fold, so the definition is general and large deviations in coordinates are tolerated. A user supplies a matrix for a motif, and ProSMoS lists all structures that exactly match this motif.
Multiple alignment of protein binding sites recognizes spatial chemical binding patterns common to a Set of protein Structures.
SiteEngine recognizes regions on the surface of one protein that resemble a specific binding site of another.
Patterns In Non-homologous Tertiary Structures. PINTS finds similarities between protein structures consisting of amino acids that are close in space, but not necessarily close or co-linear in sequence (local structural patterns, for example the catalytic triad). Unlike other tools, PINTS does not aim to find proteins adopting a similar fold.
FunClust is a web server for the identification of local functional motifs in a set of non homologous protein structures
The LabelHash suite of programs and scripts can be used to match point-based structural motifs to a set of target proteins. A motif is defined by the C-alpha positions of a number of residues. Associated with each motif point is a number of allowed residue labels.
RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by a 3D motif given in input.
Given a set of motifs and a reference sequence, seeMotif helps to visualize and exploring these motifs in appropriate structures selected based on a reference sequence.
ProtMot, a PROTeins MOTif analysis tool. This web site analyzes structure of proteins and output the list of hydrogen bonding patterns network motifs. The list of motifs, a superset of the secondary structures, is shown both projected on the protein structure and as a network motif significance profile (SP), a chart which gives the occurrences of each motif in the protein.
Interface Analysis
PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins. It permits the classification of proteins according to their interaction properties.
PDBePISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters.
Multiple Alignment of Protein-Protein InterfaceS recognizes spatially conserved chemical interactions shared by a set of protein-protein interfaces.
Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites.
A Macromolecular Interface Navigator. MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. MolSurfer can be used to study protein-protein and protein-DNA/RNA interfaces. The 2D projections of the computed interface aid visualization of complicated interfacial geometries in 3D. Molecular properties, including hydrophobicity and electrostatic potential, can be projected onto the interface. MolSurfer can thereby aid exploration of molecular complementarity, identification of binding 'hot spots' and prediction of the effects of mutations. MolSurfer can also facilitate the location of cavities at macromolecular interfaces.
A server for the analysis of the physicochemical features of protein-protein interfaces.
AquaProt analyses protein-protein binding interface, defines inter-residue interaction map within the interface and extracts related water molecules.
VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions.
LIGPLOT Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file.
Contact Maps
NNcon: Protein Contact Map Prediction Using Artificial Neural Networks.
Solvent Accessibility
Solvent accessibility based Protein-Protein Interface iDEntification and Recognition.
Accurate sequence-based prediction of relative Solvent AccessiBiLitiEs, secondary structures and transmembrane domains for proteins of unknown structure.
Calculation of Solvent Accessible Surface Areas, Atomic Solvation Energies and Their Gradients for Macromolecules.
POPS is a fast algorithm to calculate solvent accessible surface areas (SASAs) of proteins and nucleic acids at atomic (default) and residue (coarse-grained) level.
This server provides graphical representation of solvent accessibility of amino acid residues in proteins, with known structures.
Functional & Conserved Residues
The ConSurf server is a useful and user-friendly tool that enables the identification of functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure, based on the phylogenetic relations between its close sequence homologues.
Crescendo can only be used to identify residues that are interacting with ligands or other proteins.
Effects of Mutations
Prediction of Protein Stability Changes for Single-Site Mutations from Sequences
FoldX provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.
SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations.
Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein. It calculates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins.
The server predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs.
CUPSAT is a tool to predict 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.
RANK 50
SNAP is a method for evaluating effects of single amino acid substitutions on protein function. It was developed by Yana Bromberg in Rost Lab, at Columbia University, New York.
Disulphide Bonds
Cysteines Disulfide Bonding State and Connectivity Predictor
DiANNA: unified software for Cysteine state and Disulfide Bond partner prediction
Disulfide by Design is an application for the rational design of disulfide bonds in proteins. For a given protein structural model, all residue pairs are rapidly assessed for proximity and geometry consistent with disulfide formation
Predicting the redox state of cysteins in proteins from multiple sequence alignments
DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.
Metal Bindind Sites
MetalDetector predicts metal binding sites in proteins using sequence information alone. Prediction is limited to transition metals (with the addition of heme and Fe/S clusters) and to CYS and HIS as ligands.
This site uses the 'CHED' algorithm to predict 3D intra-chain protein binding sites for transition metals (Zn, Fe, Mn, Cu, Ni, Co, and Ca and Mg sites that can be replaced by a transition metal).
The Web Bench
The Web Bench
is the essential companion to the biologist, bringing informational resources and a collection of tools & calculators to facilitate work at the bench and analysis of biological data.
Check out the full online bench here
Check out the full online bench here
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