|
"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.
|
| |
|
|
AS-ALPS -- Alternative Splicing-induced ALteration of Protein Structure database
|
| Find information about the roles that alternative splicing variants play in protein structure and function.
|
| |
|
|
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.
|
| |
|
|
CC+ -- Coiled-coil protein structures database
|
| Find information about sequence-to-structure relationships in coiled-coil protein structures.
|
| |
|
|
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.
|
| |
|
|
CPDB -- Circular Permutation in Proteins Database
|
| Search for information about circular permutation (CP) and CP relationships among 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.
|
| |
|
|
Con-Struct Map -- a comparative contact map analysis tool
|
| A graphical tool for the comparative study of 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 -- Genomes to Protein structures and functions database
|
| 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.
|
| |
|
|
JAIL -- Just Another Interface Library
|
| Find information about macromolecule interfaces and molecule recognition.
|
| |
|
|
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.
|
| |
|
|
KineticDB -- Protein folding kinetics database
|
| Find information about experimental protein folding rates.
|
| |
|
|
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 -- 3D Protein Models Database
|
| 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.
|
| |
|
|
MeDor -- Metaserver of Disorder
|
| A metaserver for predicting protein disorder.
|
| |
|
|
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.
|
| |
|
|
MetalDetector -- Cysteines and Histidines Bonding State Predictor
|
| A web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
|
| |
|
|
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 -- Protein Database Summaries
|
| At-a-glance overview of every macromolecular structure deposited in the Protein Data Bank.
|
| |
|
|
PEDANT -- 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.
|
| |
|
|
POLYVIEW-3D -- Versatile annotation and publication quality visualization of protein complexes
|
| A new tool for protein structure analysis.
|
| |
|
|
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.
|
| |
|
|
POODLE-S -- Predicition Of Order and Disorder by machine LEarning
|
| Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.
|
| |
|
|
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, ø, ÷1, and ù 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.
|
| |
|
|
PSI SGKB -- The Protein Structure Initiative Structural Genomics Knowledgebase
|
| Designed to turn the products of the Protein Structure Initiative into knowledge that is important for understanding living systems and disease.
|
| |
|
|
ParCrys -- protein crystallization propensity prediction
|
| A Parzen Window approach to estimate a protein's propensity to produce diffraction-quality crystals.
|
| |
|
|
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.
|
| |
|
|
RsiteDB -- RNA binding sites database
|
| Find information about protein binding pockets that interact with RNA nucleotides.
|
| |
|
|
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.
|
| |
|
|
SPROUTS -- Structural Prediction for Protein Folding Utility System
|
| Use this tool to predict protein structures.
|
| |
|
|
SRide -- a server for identifying stabilizing residues in proteins
|
| Identify stabilizing residues in protein structures.
|
| |
|
|
SSEP -- secondary structural elements of proteins
|
| Access information related to the protein secondary structural elements present in the 25 and 90% non-redundant protein chains.
|
| |
|
|
STING Report -- convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database
|
| Extract and present detailed information about any individual amino acid of a protein structure stored in the STING Database.
|
| |
|
|
STRIDE -- A web server for secondary structure assignment from known atomic coordinates of proteins
|
| Conduct the secondary structure assignment from atomic resolution protein structures.
|
| |
|
|
SUPERFAMILY -- Protein Structural Database
|
| Database of structural and functional protein annotations for all completely sequenced organisms.
|
| |
|
|
SURFACE -- SUrface Residues and Functions Annotated, Compared and Evaluated
|
| Compare annotated protein surface regions and find putative surface functional sites.
|
| |
|
|
SWISS-MODEL -- an automated protein homology-modeling server
|
| Conduct automated comparative modeling of three-dimensional (3D) protein structures.
|
| |
|
|
SWISS-MODEL Repository -- Annotated 3D Protein Structure Homology Models
|
| Search for annotated 3D protein structural information of proteins.
|
| |
|
|
Scooby-domain -- prediction of globular domains in protein sequence
|
| Identify globular domains in protein sequences.
|
| |
|
|
Servers for sequence–structure relationship analysis and prediction
|
| Analyze and predict various features of protein structures based on protein sequences.
|
| |
|
|
SitesBase -- a database for structure-based protein–ligand binding site comparisons
|
| Search for known ligand binding sites of proteins within the PDB. |
| |
|
|
SledgeHMMER -- A web server for batch searching the Pfam database
|
| Carry out batch searching of Pfam database using the 'hmmpfam' program.
|
| |
|
|
Spritz -- a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines
|
| Predict disordered regions from a protein sequence.
|
| |
|
|
Static benchmarking of membrane helix predictions
|
| Evaluate new methods for membrane helix structure prediction using a standard set of evaluations that test many aspects of TMH prediction.
|
| |
|
|
SuperPose -- a simple server for sophisticated structural superposition
|
| Perform protein sequence and structure alignment.
|
| |
|
|
Superimpose -- a 3D structural superposition server
|
| Performs structural similarity searches with a preference towards 3D structure-based methods.
|
| |
|
|
Swiss EMBnet node web server
|
| Use a collection of bioinformatics tools at this portal site. |
| |
|
|
TMB-Hunt -- a web server to screen sequence sets for transmembrane ß-barrel proteins
|
| Identify transmembrane beta-barrel proteins (ß-barrel) based on protein sequences.
|
| |
|
|
TMBETA-GENOME -- database for annotated ß-barrel membrane proteins in genomic sequences
|
| Search for predicted and annotated beta-barrel membrane proteins (TMBs) for all completed genomes.
|
| |
|
|
TMBETA-NET -- discrimination and prediction of membrane spanning ß-strands in outer membrane proteins
|
| Discriminate outer membrane proteins and predict their membrane spanning ß-strand segments.
|
| |
|
|
TMHMM Server v. 2.0 -- Prediction of transmembrane helices in proteins
|
| Predict transmembrane helices in proteins.
|
| |
|
|
TMPDB -- A database of experimentally-characterized transmembrane topologies
|
| Search for information about experimentally-characterized transmembrane (TM) topologies |
| |
|
|
TMpro -- transmembrane helix prediction
|
| Transmembrane helix prediction through amino acid property analysis.
|
| |
|
|
TOPDB -- topology data bank of transmembrane proteins
|
| Search a collection of transmembrane protein datasets containing experimentally derived topology information.
|
| |
|
|
TOPS -- An Enhanced Database of Protein Structural Topology
|
| Search topological descriptions of protein structures and visualize folding topologies.
|
| |
|
|
TRAMPLE -- the transmembrane protein labeling environment
|
| Predict and annotate transmembrane protein sequences.
|
| |
|
|
TargetDB -- Target data from worldwide structural genomics projects
|
| Search for protein target data from the NIH structural genomics centers and a number of international sites.
|
| |
|
|
The ASTRAL Compendium
|
| To search and analyze protein structure domains.
|
| |
|
|
The CATH database -- Class, Architecture, Topology, and Homology Protein Structure Database
|
| Search for information on protein domain structures and classification.
|
| |
|
|
The FoldX web server -- an online force field
|
| Conduct rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids.
|
| |
|
|
The HHpred interactive server for protein homology detection and structure prediction
|
| Detect homology and predict structures among distantly related proteins.
|
| |
|
|
The IMB Jena Image Library of Biological Macromolecules
|
| Access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB).
|
| |
|
|
The Jpred 3 secondary structure prediction server
|
| A secondary structure prediction server powered by the Jnet algorithm.
|
| |
|
|
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
|
| Conduct various analysis to protein sequences use a suite of software tools. |
| |
|
|
The MPI Bioinformatics Toolkit for protein sequence analysis
|
| Conduct protein sequence and structure analysis using a suite of software tools. |
| |
|
|
The PMDB Protein Model Database
|
| Search for manually built 3D models of proteins.
|
| |
|
|
The PSSH database of alignments between protein sequences and tertiary structures
|
| Investigate the tertiary structure of a protein of interest.
|
| |
|
|
The PredictProtein server
|
| Predict protein structure and function based on protein sequence. |
| |
|
|
The PredictProtein server
|
| Predict protein structure and function based on protein sequence. |
| |
|
|
The RCI server -- rapid and accurate calculation of protein flexibility using chemical shifts
|
| Predict protein flexibility by calculating the Random Coil Index from backbone chemical shifts.
|
| |
|
|
The SBASE domain sequence library -- Domain architecture prediction
|
| Search for protein domain sequences, structures, functions,etc. |
| |
|
|
The Structure Superposition Database
|
| Search and visualize protein structure superpositions.
|
| |
|
|
The web server of IBM's Bioinformatics and Pattern Discovery group
|
| Access to a large number of software tools for various bioinformatics tasks.
|
| |
|
|
Tools for comparative protein structure modeling and analysis
|
| Conduct comparative protein structure modeling and analysis.
|
| |
|
|
UMMS -- constrained harmonic and anharmonic analyses of macromolecules based on elastic network models
|
| Conduct harmonic and/or anharmonic analyses of protein structures.
|
| |
|
|
VADAR -- a web server for quantitative evaluation of protein structure quality
|
| Conduct automated quantitative protein structure evaluation.
|
| |
|
|
VMD -- Visual Molecular Dynamics
|
| A molecular visualization and analysis program.
|
| |
|
|
Voronoia -- Voronoi Cell Protein Packing Database
|
| Analyze and visualize the atomic packing of protein structures.
|
| |
|
|
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations
|
| Use several Web servers to conduct various protein modeling and protein structure analysis.
|
| |
|
|
WebFEATURE -- an interactive web tool for identifying and visualizing functional sites on macromolecular structures
|
| Scan query structures for functional sites in both proteins and nucleic acids.
|
| |
|
|
Wordom -- a program for efficient analysis of molecular dynamics simulations
|
| A program for a broad range of types of analysis of molecular dynamics trajectories.
|
| |
|
|
Wurst -- A protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
|
| Perform protein sequence to structure alignments to a library.
|
| |
|
|
XtalPred -- a web server for prediction of protein crystallizability
|
| Prediction of protein crystallizability.
|
| |
|
|
eF-seek -- prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
|
| Predict the functional sites of proteins.
|
| |
|
|
eF-site -- Electrostatic surface of Functional site
|
| Identify the protein surface around the functional site and to estimate the biochemical function.
|
| |
|
|
fastSCOP -- a fast web server for recognizing protein structural domains and SCOP superfamilies
|
| Input a protein structure as a query to assign the SCOP domains and evolutionary classifications.
|
| |
|
|
iGNM: a database of protein functional motions based on Gaussian Network Model
|
| Search for the information on the equilibrium
dynamics at the level of individual residues for Protein Data Bank (PDB) structures.
|
| |
|
|
iMOT -- An interactive package for the selection of spatially interacting motifs
|
| Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.
|
| |
|
|
iMOTdb -- a comprehensive collection of spatially interacting motifs in proteins
|
| Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.
|
| |
|
|
iMolTalk -- An interactive, Internet-based protein structure analysis server
|
| Identify and highlight biochemically important regions in protein structures.
|
| |
|
|
iPDA -- integrated protein disorder analyzer
|
| Identify the disordered regions of a query protein.
|
| |
|
|
iProClass -- An integrated database of protein family, function and structure information
|
| Search for integrated and comprehensive information on family relationships and structural/functional features of proteins. |
| |
|
|
kinDOCK -- a tool for comparative docking of protein kinase ligands
|
| Fit of ligands into the ATP-binding site of a protein kinase and identify its potential ligands.
|
| |
|
|
oGNM: online computation of structural dynamics using the Gaussian Network Model
|
| 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).
|
| |
|
|
pKNOT -- the protein KNOT web server
|
| Locate info on knotted proteins.
|
| |
|
|
pdbFun -- mass selection and fast comparison of annotated PDB residues
|
| Perform and functional analysis of proteins at the residue level.
|
| |
|
|
piSite -- database of Protein Interaction Sites
|
| Find information about protein binding pockets.
|
| |
|
|
pvSOAR -- Detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
|
| Identify similar protein surface regions.
|
| |
|
|
sgTarget -- a target selection resource for structural genomics
|
| Select and prioritize targets for protein structure determination.
|
| |
|
|
transFold -- a web server for predicting the structure and residue contacts of transmembrane beta-barrels
|
| Predict the super-secondary structure of Transmembrane beta-barrel (TMB).
|
| |
|
|
wwPDB -- The worldwide Protein Data Bank
|
| Search within an international collaboration that manages the deposition, processing and distribution of the PDB archive.
|
| |
