"DAS" - Transmembrane Prediction server
Find the presence of transmembrane regions in an amino acid sequence.
 
(PS)2 -- Protein Structure Prediction Server
Predict protein structures based on consensus sequences.
 
3D-Fun -- predicting enzyme function from structure
Predict protein function from structure.
 
3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes
Compare structural and functional annotations of proteins between sequenced genomes.
 
3D-partner -- a web server to infer interacting partners and binding models
Predict interacting partners and binding models.
 
3DID -- 3D interacting domains
Search for domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
 
3MOTIF -- a protein structure visualization system for conserved sequence motifs
Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.
 
3dLOGO -- a web server for the identification, analysis and use of conserved protein substructures
Identify and analyze conserved protein 3D substructures.
 
3dSS -- 3D structural superposition
Superpose two or more 3D structures.
 
A Protein Classification Benchmark collection for machine learning
Use standard datasets to compare protein classification by different machine learning methods.
 
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
Align and compare protein structures using the Combinatorial Extension (CE) algorithm.
 
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
Compare pairs of protein polypeptide chains and obtains a list of structurally similar proteins along with their structure alignments.
 
AISMIG — an interactive server-side molecule image generator
Generate and visualize high quality molecular structure images.
 
AS2TS system for protein structure modeling and analysis
Perform homology-based protein structure analysis and modeling.
 
AffinDB -- a freely accessible database of affinities for protein–ligand complexes from the PDB
Search for affinity data for structurally resolved protein–ligand complexes from the Protein Data Bank (PDB).
 
Anisotropic Network Model web server
Predict potential flexibility and mobility of each amino acid present in a protein sequence
 
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
Detect of local structural patterns in proteins.
 
ArchDB -- Automated Protein Loop Classification as a Tool for Structural Genomics
To search protein with classified loops.
 
ArchPRED -- a template based loop structure prediction server
Predict protein loop structure.
 
AutoPSI -- Automated Protein Structure Identification
Database for automatic structural classification of protein sequences and structures
 
BAliBASE -- Benchmark Alignment dataBASE
Evaluate sequence alignment using the benchmark alignment database.
 
BOMP -- A Program to Predict Integral ß-barrel Outer Membrane Proteins Encoded within Genomes of Gram-negative Bacteria
Predict whether or not a polypeptide sequence from a Gram-negative bacterium is an integral ß-barrel outer membrane protein.
 
BPROMPT -- a consensus server for membrane protein prediction
Predict membrane proteins structures and topology.
 
BSDD -- Biomolecules Segment Display Device—a web-based interactive display tool
Search for and visualize a user-defined motif or fragment among the protein structures available in the Protein Data Bank.
 
BhairPred -- prediction of ß-hairpins in a protein from multiple alignment information using ANN and SVM techniques
Predict a super secondary structural motif, ß-hairpins, in a protein sequence.
 
Binding MOAD -- Mother of All Databases
Database of 9836 protein-ligand crystal structures.
 
BioInfo3D -- A suite of tools for structural bioinformatics
Analyze protein structures.
 
BioMagResBank -- a repository for data from NMR spectroscopic studies of biological molecules
Search for structural information of proteins, peptides, and nucleic acids based on NMR spectroscopic data.
 
Biological Macromolecule Crystallization Database
Search for information on the structures and crystallization conditions for 3547 crystal entries from 2526 biological macromolecules.
 
Building protein diagrams on the web with the residue-based diagram editor RbDe
Construct schematic diagrams of proteins.
 
CADB -- Conformation Angles DataBase of proteins
Access data on conformation angles (both main-chain and side-chain) of protein structures.
 
CAMPO, SCR_FIND and CHC_FIND -- a suite of web tools for computational structural biology
Identify evolutionarily conserved features of protein structures using three software tools.
 
CARGO -- A web portal to integrate customized biological information
A open platform system that aims to facilitate the analysis of biological data, including visualization, mapping, and literature retrieval.
 
CASTp -- computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.
 
CE-MC -- A Multiple Protein Structure Alignment Server
Align multiple protein structures based on C-alpha coordinate distances, using combinatorial extension (CE) and Monte Carlo (MC) optimization methods.
 
CKAAPs DB -- A Conserved Key Amino Acid Positions DataBase
Find key residues in common folds from structurally similar proteins with dissimilar sequences.
 
COLORADO3D -- A web server for the visual analysis of protein structures
Directly and visually analyze various features in three-dimensional protein structures.
 
CS23D -- chemical shift to 3D structure
A web server for rapid protein structure generation using NMR chemical shifts and sequence data.
 
CUPSAT -- prediction of protein stability upon point mutations
Analyze and predict protein stability changes upon point mutations.
 
CX, DPX and PRIDE -- WWW servers for the analysis and comparison of protein 3D structures
Analyze protein 3D structures submitted by the users as the Protein Data Bank (PDB) files.
 
CaspR -- A web server for automated molecular replacement using homology modeling
Optimize molecular replacement procedure using a combination of well-established stand-alone software tools.
 
CoC Central -- A database of universally conserved residues in protein folds
Search for residue conservation data covering the universe of known protein structures.
 
ConPred II -- A Consensus Prediction Method for Obtaining Transmembrane Topology Models with High Reliability
Predict transmembrane topology [i.e. the number of TM segments (TMSs), TMS positions and N-tail location] based on a consensus approach by combining the results of several proposed methods.
 
CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography
Perform phase extension and refinement in X-ray crystallography
 
CyBase -- a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
Search for curated sequence and structure information on cyclic proteins.
 
CysView -- Protein Classification Based on Cysteine Pairing Patterns
Identify and classify proteins according to their disulfide connectivity patterns.
 
DBAli -- A Database of Structure Alignments
Mine the protein structure space.
 
DHcL -- Domain Hierarchy and closed Loops
Explore th hierarchy of protein domain structure.
 
DIAL -- a web-based server for the automatic identification of structural domains in proteins
Automatically identify protein structural domains given the three-dimensional coordinates of a protein.
 
DICHROWEB -- An online server for protein secondary structure analyses from circular dichroism spectroscopic data
Perform analyses of circular dichroism spectroscopic data.
 
DISULFIND -- a disulfide bonding state and cysteine connectivity prediction server
Predict disulfide bonding state of cysteines and their disulfide connectivity from a protein sequence.
 
DMAPS -- a database of multiple alignments for protein structures
Search for pre-computed multiple structure alignments for protein chains in the Protein Data Bank (PDB).
 
DSDBASE -- A Consortium of Native and Modeled Disulphide Bonds in Proteins
To search for information on native disulphides and those that are stereochemically possible between pairs of residues for all known protein structural entries.
 
DSMM -- A Database of Simulated Molecular Motions
Search for information about movies showing biomolecular motions that have been generated by computer simulation.
 
DSSPcont -- continuous secondary structure assignments for proteins
Perform automated protein secondary structure assignment from PDB structures.
 
Dali fold classification
Search for information on protein classification and structural alignments.
 
Database of Protein Disorder -- proteins that lack fixed 3D structure in their native states
Search for curated information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
 
Decoys 'R' Us
Use computationally generated hypothetical protein sequences to improve protein structure prediction.
 
Detection of reliable and unexpected protein fold predictions using 3D-Jury
Predict protein structures using a fully automated protein structure meta prediction system accessible via the Meta Server interface.
 
DiANNA -- unified software for Cysteine state, Disulfide Bond partner prediction and ternary cysteine classification
Predict the disulfide bond topology and partner in a protein based on its sequence.
 
DomIns -- A Web Resource for Domain Insertions in Known Protein Structures
To search for domain insertions in known protein structures that are classified in the SCOP database.
 
E-MSD -- The Macromolecular Structure Database
Search macromolecular structure data in the Protein Data Bank (PDB) and other integrated bioinformatics data resources.
 
ESPript/ENDscript -- extracting and rendering sequence and 3D information from atomic structures of proteins
Generate multiple sequence alignments adorned with secondary structure elements in high quality PostScript graph.
 
EVA -- evaluation of protein structure prediction servers
Evaluate the accuracy of automated protein structure prediction methods.
 
EVAcon -- a protein contact prediction evaluation service
Continuously and automatically analyze protein inter-residue contact prediction servers in real time.
 
EXPASY Proteome Tools Collection
Use a collection of tools for protein analyses.
 
ElNémo -- A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
Compute the low frequency normal modes of a protein in PDB format.
 
Enlarged FAMSBASE -- Protein 3D structure models of genome sequences for 41 species
Search for 3D protein structure models for the whole genome of 41 species.
 
FATCAT -- A web server for flexible structure comparison and structure similarity searching
Conduct flexible protein structure comparison.
 
FOLD-RATE -- prediction of protein folding rates from amino acid sequence
Predict protein folding rates based on amino acid sequence.
 
FRalanyzer -- Fold Recognition alignment analyzer
A tool for functional analysis of fold-recognition sequence-structure alignments.
 
FastContact 2.0:a free energy scoring tool for protein-protein complex structures
Estimates the direct electrostatic and desolvation interaction free energy between two proteins.
 
FeatureMap3D — a tool to map protein features and sequence conservation onto homologous structures in the PDB
Combine protein sequence-based information with structural data from the Protein Data Bank (PDB).
 
FirstGlance in Jmol
Use this simple 3D tool to visualize macromolecular structures.
 
Flexible Structural Neighborhood — a database of protein structural similarities and alignments
Search for structural neighbors of proteins.
 
FoldMiner and LOCK 2 -- Protein structure comparison and motif discovery on the web
Perform protein structure alignment and unsupervised motif discovery.
 
Fragment Finder -- a web-based software to identify similar three-dimensional protein structural motif
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.
 
Fragnostic -- walking through protein structure space
Discover structural and functional relationships between proteins which are distantly related or seemingly unrelated.
 
Frog -- a FRee Online druG 3D conformation generator
 
GDAP -- A Web Tool for Genome-wide Protein Disulfide Bond Prediction
Predict protein disulfide bonds in protein sequences.
 
GTD -- The Genomic Threading Database
To search for structural annotation for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes.
 
GTOP -- a database of protein structures predicted from genome sequences
Use sequence homology analyses to predict protein structures and functions.
 
GenDiS -- Genomic Distribution of protein structural domain Superfamilies
Identify and classify evolutionary related proteins at the superfamily level in whole genome databases.
 
Gene3D -- comprehensive structural and functional annotation of genomes
Find structural and functional annotation of most available protein sequences.
 
GeneSilico protein structure prediction meta-server
Predict protein structures use this gateway, which combines the useful features of other meta-servers available, but with much greater flexibility of the input.
 
Geno3D -- Protein Modeling Tool
Predict the 3D structure of an amino acid sequence.
 
GlobPlot -- exploring protein sequences for globularity and disorder
Discover unstructured or disordered regions within proteins.
 
GlyProt -- in silico glycosylation of proteins
Connect N-glycans in silico to a given 3D protein structure.
 
HARMONY -- a server for the assessment of protein structures
Examine the compatibility between the sequence and the three-dimensional structure of a protein.
 
HELIQUEST -- a web server to screen sequences with specific {alpha} -helical properties
Identify protein segments possessing similar features.
 
HOMSTRAD -- the Homologous Protein Structure Alignment Database
To identify key structurally conserved residues within the same protein families.
 
HPD -- the Heme Protein Database
A resource of heme protein structure-function relationships.
 
HSSP -- Homology derived Secondary Structure of Proteins
Search for information of aligned protein sequence families and their secondary and tertiary structures.
 
Het-PDB Navi. -- a database for protein-small molecule interactions
Search for information on the interactions between proteins and small molecules.
 
I-Mutant 2.0 -- predicting stability changes upon mutation from the protein sequence or structure
Predict protein stability changes upon single point mutations in protein sequence.
 
IMGT/3Dstructure DB and IMGT/StructuralQuery -- A Database and A Tool for Immunoglobulin, T Cell Receptor and MHC Structural Data
To search for structural information on immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species.
 
Integrated databanks access and sequence/structure analysis services at the PBIL
Access to sequence databanks and to many tools of nucleic acid and protein sequence analyses.
 
JavaProtein Dossier -- A novel web-based data visualization tool for comprehensive analysis of protein structure
Visualize and analyze protein structures.
 
KUJIRA -- a program for analysis of NMR data
A package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.
 
LGA -- a method for finding 3D similarities in protein structures
Compare protein structures or fragments of protein structures in sequence dependent and sequence independent modes.
 
LPFC -- A Library of Protein Family Cores
Search for computed average core structures for each protein family.
 
LigASite -- LIGand Attachment SITE
Database of biologically relevant binding sites in proteins with known apo-structures
 
LocalMove -- computing on-lattice fits for biopolymers
Determine an on-lattice representation for an input biomolecule.
 
Localizome -- a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
Predict the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein.
 
M4T -- Multiple Mapping Method with Multiple Templates
A comparative protein structure modeling server.
 
MAPPIS -- Multiple Alignment of Protein-Protein InterfaceS
Recognize spatially conserved chemical interactions shared by a set of PPIs.
 
MATRAS -- a program for protein 3D structure comparison
Compare protein 3D structures.
 
MDB -- The Metalloprotein Database and Browser at The Scripps Research Institute
Search for quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank.
 
MEDock -- a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
Predict ligand binding sites in protein molecules with a Maximum-Entropy based docking Web server.
 
META-PP -- single interface to crucial prediction servers
Locate protein structure prediction servers through this portal site.
 
MMDB -- Entrez's 3D-structure database
Find the 3D structure of a protein from MMDB.
 
MODBASE -- A Database of Annotated Comparative Protein Structure Models, and Associated Resources
Search for annotated comparative protein structure models for all available protein sequences.
 
MODPROPEP -- a program for knowledge-based modeling of protein-peptide complexes
A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.
 
MOLPROBITY -- Structure validation and all-atom contact analysis for nucleic acids and their complexes
Validate macromolecular 3D structures.
 
MONSTER -- Inferring non-covalent interactions in macromolecular structures from atomic coordinate data
Infer potentially stabilizing non-bonding interactions in macromolecular structures from input atomic coordinate data.
 
MegaMotifBase -- a database of structural motifs in protein families and superfamilies
Find structural segments or motifs for protein structures.
 
MemBrain -- improving the accuracy of predicting transmembrane helices
Accurately predict transmembrane helices.
 
Membrane Protein Resources
Search for various information on membrane protein structures and topology.
 
Meta-BASIC -- Detecting distant protein homology
Detect distant similarity between proteins based on consensus alignments of meta profiles.
 
MoViES -- Molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
Analyze Vibrational Dynamics of Proteins and Nucleic Acids.
 
MolAxis -- a server for identification of channels in macromolecules
Accurate identification of channels in macromolecules.
 
MolMovDB -- Analysis and visualization of conformational change and structural flexibility
Analyze and visualize conformational change and structural flexibility of RNA and protein.
 
MolSurfer -- a macromolecular interface navigator
Analyze the structures and physico-chemical properties of macromolecular interfaces.
 
Motif3D -- Relating protein sequence motifs to 3D structure
Visualize protein sequence motifs on the 3D protein structures.
 
MovieMaker -- a web server for rapid rendering of protein motions and interactions
Generate short movies of protein motions using the PDB files.
 
Multi-Q web server for multiplexed protein quantitation
Analyze multiplexed protein quantitation data based on the iTRAQ labeling method
 
MultiBind -- Multiple Alignment of Protein Binding Sites
Recognize spatial chemical binding patterns common to a set of protein structures.
 
MutDB -- interactive structural analysis of mutation data
Integration of publicly available databases of human genetic variation with molecular features and clinical phenotype data.
 
NOMAD-Ref -- visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
Conduct normal mode calculation, even for large proteins and including all atoms, and algorithms that use normal modes for structural refinement or optimization.
 
NORSp -- predictions of long regions without regular secondary structure
Predict long protein sequence regions with NO Regular Secondary structure.
 
NPIDB -- Nucleic Acids-Protein Interaction DataBase
A database of nucleic acids-protein interactions.
 
NQ-Flipper -- recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
Detect and correct erroneous Asn and Gln rotamers.
 
NRSAS -- Nuclear Receptor Structure Analysis Servers
Analyze Nuclear Receptor structures.
 
OMSSA -- Open mass spectrometry search algorithm
Search large MS/MS datasets.
 
OPAAS -- a web server for optimal, permuted, and other alternative alignments of protein structures
Detect alternative protein structural alignments of statistical significance, including structural permutations at all levels of complexity.
 
PALI -- Integration of related sequences with protein 3D structural families
Search for structure based sequence alignments for homologous proteins of known 3-D structure.
 
PASS2 -- an automated database of Protein Alignments Organized as Structural Superfamilies
Search for sequence alignments of proteins grouped at the level of superfamilies.
 
PAST -- fast structure-based searching in the PDB
Search 3D protein structures and identify structural motifs.
 
PAT -- a protein analysis toolkit for integrated biocomputing on the web
Conduct complex protein analyses and simplify the automation of repetitive tasks using a set of integrated protein analysis tools.
 
PDB -- The Protein Data Bank and structural genomics
Search or process 3-D structure data of large molecules of proteins and nucleic acids.
 
PDB-REPRDB -- A database of representative protein chains from the Protein Data Bank
Search for information on protein chains.
 
PDB2PQR -- An automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
Automates many of the common tasks of preparing structures for continuum electrostatics calculations.
 
PDBSite -- a database of the 3D structure of protein functional sites
Search for structural and functional information on the protein functional sites.
 
PDBSiteScan -- A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.
 
PDB_Hydro -- incorporating dipolar solvents with variable density in the Poisson–Boltzmann treatment of macromolecule electrostatics
Calculate the electrostatic properties of macromolecules.
 
PDB_TM -- selection and membrane localization of transmembrane proteins in the protein data bank
Search for membrane-spanning regions and other information of transmembrane proteins with known structures.
 
PDBsum more -- new summaries and analyses of the known 3D structures of proteins and nucleic acids
Search for at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank.
 
PEDANT genome database -- Protein Extraction, Description and ANalysis Tool
Conduct genome wide functional and structural analysis.
 
PFAST -- protein fluorescence and structural toolkit
Database and programs for the analysis of protein fluorescence and structural data.
 
PFD -- a database for the investigation of protein folding kinetics and stability
Search for biophysical data relating to experimental protein folding studies.
 
PFplus -- Patch Finder Plus
A web server for extracting and displaying positive electrostatic patches on protein surfaces.
 
PIDD -- database for Protein Inter-atomic Distance Distributions
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.
 
PMG -- Protein Movie Generator
An online service able to generate high-quality pictures and animations to define simple storyboards.
 
PONGO -- a web server for multiple predictions of all-alpha transmembrane proteins
Use multiple tools to predict transmembrane protein helices.
 
POODLE-L -- Prediction Of Order and Disorder by machine LEarning
A two-level SVM prediction system for reliably predicting long disordered regions.
 
POPS -- a fast algorithm for solvent accessible surface areas at atomic and residue level
Calculate solvent accessible surface areas of proteins or nucleic acids.
 
PPG -- online generation of protein pictures and animations
Generate pictures of a protein structure using a protein structure file (PDB format).
 
PPT-DB -- the Protein property Prediction and Testing DataBase
Locate commonly predicted protein property information.
 
PRALINE -- a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
Perform multiple protein sequence alignment and integrate information from database homology searches to generate a homology-extended multiple alignment.
 
PRED-TMBB -- A Web Server for Predicting the Topology of ß-barrel Outer Membrane Proteins
Predict the transmembrane strands and the topology of ß-barrel outer membrane proteins of Gram-negative bacteria.
 
PREDITOR -- a web server for predicting protein torsion angle restraints
Predict ö, ř, ÷1, and ů TORsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology.
 
PROCOGNATE -- a cognate ligand domain mapping for enzymes
Database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.
 
PRODECOMP -- PROjection DECOMPosition
Decompositions of NMR projections for protein backbone and side-chain assignments, and structural studies.
 
PROFEAT -- a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Compute commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence.
 
PROFtmb -- a web server for predicting bacterial transmembrane beta barrel proteins
Predict transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria.
 
PROMALS3D -- web server for accurate multiple protein sequence and structure alignments
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.
 
PROMISE -- The Prosthetic groups and Metal Ions in Protein Active Sites Database
Search for comprehensive sequence, structural, functional and bibliographic information on metalloproteins and other complex proteins, with an emphasis on active site structure and function.
 
PROSPECT-PSPP -- An automatic computational pipeline for protein structure prediction
Fully automate protein structure prediction.
 
PROTCOM -- searchable database of protein complexes enhanced with domain-domain structures
Search for structural information on protein-protein complexes.
 
PROTEUS2 -- a web server for comprehensive protein structure prediction and structure-based annotation
Supports comprehensive protein structure prediction and structure-based annotation.
 
PROTINFO -- new algorithms for enhanced protein structure predictions
Predict protein tertiary structure, functional signatures, and resistance/susceptibility of protein mutants using de novo prediction and template modeling methods.
 
PatchDock and SymmDock -- servers for rigid and symmetric docking
Analyze molecular docking of proteins.
 
Pcons.net -- protein structure prediction meta server
Provides improved automated tools for protein structure prediction and analysis using consensus.
 
PepBuild -- A web server for building structure data of peptides/proteins
Help to design and generate a capped or uncapped peptide/protein with known secondary and tertiary structure.
 
Phospho3D -- a database of three-dimensional structures of protein phosphorylation sites
Search for 3D structure and functional annotation of phosphorylation sites in proteins.
 
PrDOS -- Protein DisOrder prediction System
Predict disordered protein regions from amino acid sequences.
 
Predict Protein
Perform sequence analysis and structure prediction for an amino acid sequence
 
Prediction of Coiled Coil Regions
Find the coiled-coil regions in an amino acid sequence.
 
ProFunc -- a server for predicting protein function from 3D structure
Predict protein functions based on known structures.
 
ProKware -- integrated software for presenting protein structural properties in protein tertiary structures
Display structural and functional features mapped onto protein 3D structures.
 
ProSA-web -- Protein Structure Analysis
Interactive web service for the recognition of errors in three-dimensional structures of proteins.
 
ProSAT2 — Protein Structure Annotation Server
Interactively visualize sequence-based functional annotations mapped onto protein 3D structures.
 
ProTarget -- automatic prediction of protein structure novelty
Predict novel protein folding using a Web-based tool.
 
ProteMiner-SSM -- Efficient Analysis of Similar Protein Tertiary Substructures
Analyze similar protein tertiary substructures to aid protein–ligand interactions studies.
 
Protein Block Expert (PBE) -- a web-based protein structure analysis server using a structural alphabet
Conduct protein structure analysis and comparison using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet.
 
Protein Dipole Moments Server
A server and database for dipole moments of proteins.
 
Protein Peeling 2 -- a web server to convert protein structures into series of protein units
Identify protein subunits based on 3D coordinates.
 
Protein knot server -- detection of knots in protein structures
Check PDB entries or uploaded structures to visualize protein knots.
 
Protein structure prediction servers at University College London
Analyze and predict protein structures using a number of state-of-the-art protein structure prediction servers.
 
ProteinDBS -- A real-time retrieval system for protein structure comparison
Support protein global-to-global tertiary structure matching.
 
QSCOP-BLAST -- quantitative structural classification of proteins
Fast retrieval of quantified structural information for protein sequences of unknown structure.
 
RAPIDO -- Rapid Alignment of Proteins In terms of DOmains
A web server for the alignment of protein structures in the presence of conformational changes.
 
RPBS -- a web resource for structural bioinformatics
Analyze and compare protein structures using a list of tools.
 
ReadOut -- structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition
Analyze structure of a protein-DNA complex.
 
RefDB -- Re-referenced Protein Chemical Shift
Search for reference-corrected protein chemical shifts data.
 
Robetta Server -- Protein structure prediction and analysis
Automate protein structure prediction and analysis.
 
RosettaDesign server for protein design
Identify low energy amino acid sequences for target protein structures.
 
S4 -- structure-based sequence alignments of SCOP superfamilies
Search for structure-based sequence alignments of domains in SCOP protein superfamilies.
 
SA-Search -- A web tool for protein structure mining based on a Structural Alphabet
Search for 3D fragments similar to (fragments of) a protein query structure.
 
SABBAC -- online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace
Reconstruct complete protein structures from their alpha-carbon description.
 
SCOP -- The Structural Classification of Proteins Database
Search for proteins of known structure, according to their evolutionary and structural relationships.
 
SCOPEC -- Mapping of catalytic function to domain structure
Search for information on enzyme catalytic domains.
 
SCOPPI -- a structural classification of protein-protein interfaces
Search for information on protein domain-domain interfaces and interactions.
 
SCRATCH -- a protein structure and structural feature prediction server
Predict protein tertiary structure and structural features using a suite of tools.
 
SCit -- Web tools for protein side chain conformation analysis
Analyze protein side chain conformation and positioning.
 
SDPMOD -- An Automated Comparative Modeling Server for Small Disulfide-bonded Proteins
Perform comparative modeling of small Disulphide-bonded Proteins (SDPs).
 
SEM (Symmetry Equivalent Molecules) -- A web-based GUI to generate and visualize the macromolecules.
Generate and visualize the symmetry equivalent macromolecules (proteins and nucleic acids).
 
SEQATOMS -- a web tool for identifying missing regions in PDB in sequence context
Visualize all "missing" protein regions in PDB.
 
SISYPHUS — structural alignments for proteins with non-trivial relationships
Search curated structural alignments among proteins with non-trivial structural relationship.
 
SNAPPI-DB -- a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions
Search for information on structures,interfaces and alignment of protein-protein interactions.
 
SPACE -- a suite of tools for protein structure prediction and analysis based on complementarity and environment
Predict and analyze structures of biomolecules and their complexes.