Proteins
Predict protein structures based on consensus sequences.
Perform secondary structure predictions on protein sequences.
Compare structural and functional annotations of proteins between sequenced genomes.
Find information about proteins from their surface shape.
Predict interacting partners and binding models.
Search for domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.
Superpose two or more 3D structures.
Use standard datasets to compare protein classification by different machine learning methods.
Align and compare protein structures using the Combinatorial Extension (CE) algorithm.
Generate and visualize high quality molecular structure images.
Find information about the roles that alternative splicing variants play in protein structure and function.
Perform homology-based protein structure analysis and modeling.
Search for affinity data for structurally resolved proteinx96ligand complexes from the Protein Data Bank (PDB).
Predict potential flexibility and mobility of each amino acid present in a protein sequence
Detect of local structural patterns in proteins.
To search protein with classified loops.
Predict protein loop structure.
Database for automatic structural classification of protein sequences and structures
Find information about protein-protein interaction.
Predict whether or not a polypeptide sequence from a Gram-negative bacterium is an integral xdf-barrel outer membrane protein.
Predict membrane proteins structures and topology.
Perform protein structural analysis using small protein segments.
Find information about the mechanical stretching of biomolecules.
Search for and visualize a user-defined motif or fragment among the protein structures available in the Protein Data Bank.
Predict a super secondary structural motif, xdf-hairpins, in a protein sequence.
Database of 9836 protein-ligand crystal structures.
Analyze protein structures.
Search for structural information of proteins, peptides, and nucleic acids based on NMR spectroscopic data.
Search for information on the structures and crystallization conditions for 3547 crystal entries from 2526 biological macromolecules.
Construct schematic diagrams of proteins.
Access data on conformation angles (both main-chain and side-chain) of protein structures.
Identify evolutionarily conserved features of protein structures using three software tools.
A open platform system that aims to facilitate the analysis of biological data, including visualization, mapping, and literature retrieval.
Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
Find information about sequence-to-structure relationships in coiled-coil protein structures.
Find information about the conformational dynamics of large proteins and protein complexes.
Align multiple protein structures based on C-alpha coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods.
Compare protein structures.
Directly and visually analyze various features in three-dimensional protein structures.
Retrieve information about protein structural similarity.
Search for information about circular permutation (CP) and CP relationships among protein structures.
A web server for rapid protein structure generation using NMR chemical shifts and sequence data.
Analyze and predict protein stability changes upon point mutations.
Analyze protein 3D structures submitted by the users as the Protein Data Bank (PDB) files.
Optimize molecular replacement procedure using a combination of well-established stand-alone software tools.
Find information about the structure of proteins in their bound and unbound states.
Search for curated sequence and structure information on cyclic proteins.
Mine the protein structure space.
A knowledge-based method for the prediction of DNA-protein interactions.
Explore th hierarchy of protein domain structure.
Automatically identify protein structural domains given the three-dimensional coordinates of a protein.
Perform analyses of circular dichroism spectroscopic data.
Predict disulfide bonding state of cysteines and their disulfide connectivity from a protein sequence.
An accurate protein domain prediction server.
Database of known and predicted protein domain (domain-domain) interactions.
To search for information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries.
Search for information about movies showing biomolecular motions that have been generated by computer simulation.
Perform automated protein secondary structure assignment from PDB structures.
Search for curated information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
Use computationally generated hypothetical protein sequences to improve protein structure prediction.
Predict the disulfide bond topology and partner in a protein based on its sequence.
To search for domain insertions in known protein structures that are classified in the SCOP database.
Search macromolecular structure data in the Protein Data Bank (PDB) and other integrated bioinformatics data resources.
Find information about protein and other macromolecular structure data obtained through cyro electron microscopy.
Generate multiple sequence alignments adorned with secondary structure elements in high quality PostScript graph.
Evaluate the accuracy of automated protein structure prediction methods.
Continuously and automatically analyze protein inter-residue contact prediction servers in real time.
Use a collection of tools for protein analyses.
Compute the low frequency normal modes of a protein in PDB format.
Predict protein folding rates based on amino acid sequence.
Find information about how proteins dock with each other.
Estimates the direct electrostatic and desolvation interaction free energy between two proteins.
Combine protein sequence-based information with structural data from the Protein Data Bank (PDB).
Use this simple 3D tool to visualize macromolecular structures.
Search for structural neighbors of proteins.
Perform protein structure alignment and unsupervised motif discovery.
Use a Web-based interactive search engine to retrieve the user desired similar 3D structural fragments from a selected subset of 25 or 90% non-homologous protein chains.
Discover structural and functional relationships between proteins which are distantly related or seemingly unrelated.
Produce 3D conformations of small drug compounds.
Predict protein disulfide bonds in protein sequences.
Perform protein structure alignment.
To search for structural annotation for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes.
Use sequence homology analyses to predict protein structures and functions.
Find structural information on interacting proteins.
Generate 3D protein structures using NOE-derived distance restraints and NMR chemical shifts
Identify and classify evolutionary related proteins at the superfamily level in whole genome databases.
Find structural and functional annotation of most available protein sequences.
Predict protein structures use this gateway, which combines the useful features of other meta-servers available, but with much greater flexibility of the input.
Predict the 3D structure of an amino acid sequence.
Discover unstructured or disordered regions within proteins.
Connect N-glycans in silico to a given 3D protein structure.
Find information about glycans.
Examine the compatibility between the sequence and the three-dimensional structure of a protein.
Identify protein segments possessing similar features.
To identify key structurally conserved residues within the same protein families.
A resource of heme protein structure-function relationships.
Search for information on the interactions between proteins and small molecules.
Find information about potential protein structure homologs.
Database of computational hot spots in protein interfaces.
Predict protein stability changes upon single point mutations in protein sequence.
I-TASSER (Iterative Threading ASSEmbly Refinement) is an internet service for protein structure and function predictions.
Search for structural information on immune system proteins.
Access to sequence databanks and to many tools of nucleic acid and protein sequence analyses.
Find information about macromolecule interfaces and molecule recognition.
Visualize and analyze protein structures.
Interactive forecasting of protein interaction hot spots.
A package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.
Find information about experimental protein folding rates.
Compare protein structures or fragments of protein structures in sequence dependent and sequence independent modes.
Search for computed average core structures for each protein family.
Database of biologically relevant binding sites in proteins with known apo-structures
Determine an on-lattice representation for an input biomolecule.
Predict the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein.
A comparative protein structure modeling server.
Recognize spatially conserved chemical interactions shared by a set of PPIs.
Predict ligand binding sites in protein molecules with a Maximum-Entropy based docking Web server.
Locate protein structure prediction servers through this portal site.
Find information about protein structure similarity.
Find the 3D structure of a protein from MMDB.
Search for annotated comparative protein structure models for all available protein sequences.
A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.
Validate macromolecular 3D structures.
Infer potentially stabilizing non-bonding interactions in macromolecular structures from input atomic coordinate data.
Find structural segments or motifs for protein structures.
Accurately predict transmembrane helices.
Search for various information on membrane protein structures and topology.
A web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
Generate the most probable trajectory between two states.
Analyze Vibrational Dynamics of Proteins and Nucleic Acids.
Accurate identification of channels in macromolecules.
Compare the binding sites, cavities or any arbitrary residue selection of molecular surfaces.
Analyze and visualize conformational change and structural flexibility of RNA and protein.
Analyze the structures and physico-chemical properties of macromolecular interfaces.
Visualize protein sequence motifs on the 3D protein structures.
Generate short movies of protein motions using the PDB files.
Analyze multiplexed protein quantitation data based on the iTRAQ labeling method
Recognize spatial chemical binding patterns common to a set of protein structures.
Integration of publicly available databases of human genetic variation with molecular features and clinical phenotype data.
Find information about protein-protein residue contacts.
Conduct normal mode calculation, even for large proteins and including all atoms, and algorithms that use normal modes for structural refinement or optimization.
A database of nucleic acids-protein interactions.
Detect and correct erroneous Asn and Gln rotamers.
Analyze Nuclear Receptor structures.
Use to detect non-native secondary structure propensities in protein sequences.
Search large MS/MS datasets.
Find information about transition in protein structures.
Search for structure based sequence alignments for homologous proteins of known 3-D structure.
A server to predict protein active site residues.
Search for sequence alignments of proteins grouped at the level of superfamilies.
Conduct complex protein analyses and simplify the automation of repetitive tasks using a set of integrated protein analysis tools.
Find information about all the structures a given protein can take.
Find information about circular dichroism spectra.
Search or process 3-D structure data of large molecules of proteins and nucleic acids.
Search for information on protein chains.
Automates many of the common tasks of preparing structures for continuum electrostatics calculations.
Search for structural and functional information on the protein functional sites.
Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.
Calculate the electrostatic properties of macromolecules.
Search for membrane-spanning regions and other information of transmembrane proteins with known structures.
Find information about proteins from the European version of PDB, which works closely with the worldwide PDB.
Find information about unique protein chains.
At-a-glance overview of every macromolecular structure deposited in the Protein Data Bank.
Conduct genome wide functional and structural analysis.
Use to predict peptide structures from amino acid sequences.
Database and programs for the analysis of protein fluorescence and structural data.
Search for biophysical data relating to experimental protein folding studies.
A web server for extracting and displaying positive electrostatic patches on protein surfaces.
Find information about the relationship between backbone bond lengths, bond angles, and planarity of a protein and its backbone conformation.
Use to evaluate protein electrostatic characteristics in relations to molecular recognition.
Protein interface/interior prediction engine.
Explore interactions between and within proteins.
Search and analyze the statistical data for protein inter-atomic distances based on their distributions in databases of known protein structures such as in the PDB Data Bank.
Automatic prediction of antibody structures.
Find information about plant lectin domains.
An online service able to generate high-quality pictures and animations to define simple storyboards.
A new tool for protein structure analysis.
Use multiple tools to predict transmembrane protein helices.
A two-level SVM prediction system for reliably predicting long disordered regions.
Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.
Calculate solvent accessible surface areas of proteins or nucleic acids.
Generate pictures of a protein structure using a protein structure file (PDB format).
Locate commonly predicted protein property information.
Perform multiple protein sequence alignment and integrate information from database homology searches to generate a homology-extended multiple alignment.
Predict the transmembrane strands and the topology of xdf-barrel outer membrane proteins of Gram-negative bacteria.
Predict xf6, xf8, xf71, and xf9 TORsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology.
Database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.
Decompositions of NMR projections for protein backbone and side-chain assignments, and structural studies.
Construct alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
Fully automate protein structure prediction.
Supports comprehensive protein structure prediction and structure-based annotation.
Predict protein tertiary structure, functional signatures, and resistance/susceptibility of protein mutants using de novo prediction and template modeling methods.
Designed to turn the products of the Protein Structure Initiative into knowledge that is important for understanding living systems and disease.
Find information about protein structure topology.
A web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
A Parzen Window approach to estimate a protein's propensity to produce diffraction-quality crystals.
Analyze molecular docking of proteins.
Provides improved automated tools for protein structure prediction and analysis using consensus.
Search for 3D structure and functional annotation of phosphorylation sites in proteins.
Find information about protein structure.
Find information about the residues that line the pore of transmembrane proteins.
Predict disordered protein regions from amino acid sequences.
Find the coiled-coil regions in an amino acid sequence.
Predict protein functions based on known structures.
Display structural and functional features mapped onto protein 3D structures.
Interactive web service for the recognition of errors in three-dimensional structures of proteins.
A unified resource for analyzing effects of alternative splicing events in the context of protein structures.
Interactively visualize sequence-based functional annotations mapped onto protein 3D structures.
Analyze general and distant protein structural similarities.
Predict novel protein folding using a Web-based tool.
Conduct protein structure analysis and comparison using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet.
A server and database for dipole moments of proteins.
Identify protein subunits based on 3D coordinates.
Find local structure homology.
Check PDB entries or uploaded structures to visualize protein knots.
Analyze and predict protein structures using a number of state-of-the-art protein structure prediction servers.
Use to design truncation constructs of a protein under investigation.
Support protein global-to-global tertiary structure matching.
Use this server module to predict the atomic level structure of a protein complex.
Find information about the quality of protein models.
A web server for the alignment of protein structures in the presence of conformational changes.
Search for proteins with similar groups of residues that have particular topologies.
Use to predict buried versus exposed residues of helical membrane proteins.
Analyze and compare protein structures using a list of tools.
Analyze structure of a protein-DNA complex.
Search for reference-corrected protein chemical shifts data.
Automate protein structure prediction and analysis.
Use to predict antibody Fv structures.
Identify low energy amino acid sequences for target protein structures.
Predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation.
Find information about protein binding pockets that interact with RNA nucleotides.
Search for 3D fragments similar to (fragments of) a protein query structure.
Reconstruct complete protein structures from their alpha-carbon description.
Find information about human protein structures.
Find information about similar proteins based on structure, not sequence.
Use to predict 3D protein structure.
Perform sequence analysis on polyketide synthases.
Search for proteins of known structure, according to their evolutionary and structural relationships.
Search for information on enzyme catalytic domains.
Search for information on protein domain-domain interfaces and interactions.
Predict protein tertiary structure and structural features using a suite of tools.
Analyze protein side chain conformation and positioning.
Perform comparative modeling of small Disulphide-bonded Proteins (SDPs).
Generate and visualize the symmetry equivalent macromolecules (proteins and nucleic acids).
Use to predict the epitope structure of protein antigens.
Visualize all "missing" protein regions in PDB.
Search for information on structures,interfaces and alignment of protein-protein interactions.
Use this tool to predict protein structures.
Identify stabilizing residues in protein structures.
Access information related to the protein secondary structural elements present in the 25 and 90% non-redundant protein chains.
Extract and present detailed information about any individual amino acid of a protein structure stored in the STING Database.
Integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships.
Conduct the secondary structure assignment from atomic resolution protein structures.
Database of structural and functional protein annotations for all completely sequenced organisms.
Conduct automated comparative modeling of three-dimensional (3D) protein structures.
Search for annotated 3D protein structural information of proteins.
Identify globular domains in protein sequences.
Find information about populations carrying polymorphisms within protein binding pockets that make them susceptible to serious adverse drug reaction (SADR).
Visualize 3D motifs based on reference sequences.
Predict disordered regions from a protein sequence.
A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
Predict the spatial conformation of loops in membrane proteins.
Perform protein sequence and structure alignment.
Performs structural similarity searches with a preference towards 3D structure-based methods.
Use a collection of bioinformatics tools at this portal site.
Search for predicted and annotated beta-barrel membrane proteins (TMBs) for all completed genomes.
Discriminate outer membrane proteins and predict their membrane spanning xdf-strand segments.
Predict transmembrane helices in proteins.
Use to find information about membrane protein topology.
Search a collection of transmembrane protein datasets containing experimentally derived topology information.
Find information about structural genomics.
Predict and annotate transmembrane protein sequences.
Search for protein target data from the NIH structural genomics centers and a number of international sites.
To search and analyze protein structure domains.
Search for information on protein domain structures and classification.
Conduct rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids.
Detect homology and predict structures among distantly related proteins.
Access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB).
A secondary structure prediction server powered by the Jnet algorithm.
Conduct various analysis to protein sequences use a suite of software tools.
Conduct protein sequence and structure analysis using a suite of software tools.
Search for manually built 3D models of proteins.
Predict protein structure and function based on protein sequence.
Predict protein structure and function based on protein sequence.
Predict protein flexibility by calculating the Random Coil Index from backbone chemical shifts.
Search for protein domain sequences, structures, functions,etc.
Search and visualize protein structure superpositions.
Conduct comparative protein structure modeling and analysis.
Conduct automated quantitative protein structure evaluation.
A molecular visualization and analysis program.
Analyze and visualize the atomic packing of protein structures.
Scan query structures for functional sites in both proteins and nucleic acids.
Perform protein sequence to structure alignments to a library.
Prediction of protein crystallizability.
An engineered zinc finger/target site design tool.
A database server mapping nsSNPs on protein structures.
Predict the functional sites of proteins.
Identify the protein surface around the functional site and to estimate the biochemical function.
Input a protein structure as a query to assign the SCOP domains and evolutionary classifications.
An expert system for predicting ligand-binding residues in protein structures.
Search for the information on the equilibrium dynamics at the level of individual residues for Protein Data Bank (PDB) structures.
Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.
Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.
Identify and highlight biochemically important regions in protein structures.
Search for integrated and comprehensive information on family relationships and structural/functional features of proteins.
Perform protein structural similarity searches.
Fit of ligands into the ATP-binding site of a protein kinase and identify its potential ligands.
Perform polymer chemistry modeling and simulation/analysis of mass spectrometric data.
Calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM).
Locate info on knotted proteins.
Perform and functional analysis of proteins at the residue level.
Find information about protein binding pockets.
Identify similar protein surface regions.
Select and prioritize targets for protein structure determination.
Predict the super-secondary structure of Transmembrane beta-barrel (TMB).
Find information about 3D protein structure from a ligand perspective.
Search within an international collaboration that manages the deposition, processing and distribution of the PDB archive.