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URLs Protein, DNA, RNA, Glycan modeling
KEGG The KEGG GLYCAN database is a collection of experimentally determined glycan structures, has >11,000 glycan structures from a large number of eukaryotic and prokaryotic sources database
PDB-Explorer A web-based interactive map of the protein data bank in shape space online
Fitmunk Improving protein structures by accurate, automatic modeling of side-chain conformations online
ModRefiner ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement online
3D-GNOME Web service for structural modeling of the 3D genome (2016) online
ORION A web server for protein fold recognition and structure prediction using evolutionary hybrid profiles (2016) online
CoinFold Protein contact prediction and contact-assisted protein folding (input sequence) online
GPCR-ModSim A web based solution for modeling G-protein coupled receptors (includes a membrane insertion and molecular dynamics (MD) equilibration protocol) online
FALCON@home A high-throughput protein structure prediction server based on remote homologue recognition online
NPDock A web server for protein nucleic acid docking online
FoldNucleus Web server for the prediction of RNA and protein folding nuclei from their 3D structures online
GPCRserver An accurate and novel G protein-coupled receptor predictor online
RosettaMP An Integrated Framework Advancing Membrane Protein Modeling and Design online
RNAssess A web server for quality assessment of RNA 3D structures online
R3D-2-MSA R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server online
RNA-Redesign A web server for fixed-backbone 3D design of RNA online
LYRA A webserver for lymphocyte receptor structural modeling online
RBO Aleph The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. Protein structure prediction online
InteractiveROSETTA A graphical user interface for the PyRosetta protein modeling suitee standalone
iceLogo The iceLogo web server and SOAP service for determining protein consensus sequences online
Modorama MODexplorer an integrated tool for exploring protein sequence, structure and function relationships (2013) and MODalign (a rich target-template alignment editor 2012) online
miRClassify An advanced web server for miRNA family classification and annotation online
MicroRNA MicroRNA discovery by similarity search to a database of RNA-seq profiles database
PETfold The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences online
CompaRNA A server for continuous benchmarking of automated methods for RNA secondary structure prediction online
RNA tool CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences online
RNA tool CentroidFold Web application online
RNA tool IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming online
RNA tool The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data online
RNA tool RSIM, an improved RNA fragment assembly method online
RNAMoIP Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure standalone
RNA tool iFoldRNA: three-dimensional RNA structure prediction and folding online
RNA tool ModeRNA server: A server for RNA structure modeling and analysis online
RNA tool RNAComposer: Automated 3D structure composition for large RNAs online
PFP Protein fingerprint generation: calculates a novel fingerprint for proteins and, optionally, compares the fingerprints of two proteins for best match standalone
MPACK This Modeling Package is an integrated protein modeling suite that currently handles comparative and ab initio modeling procedures standalone - links to other fold recognition servers
e-RNA A collection of web servers for comparative RNA structure prediction and visualisation online
RNApdbee A webserver to derive secondary structures from pdb files of knotted and unknotted RNAs online
ModWeb ModWeb: A Server for Protein Structure Modeling with Modeller (requires login account) online
BHAGEERATH-H Combination of ab initio folding and homology methods online
TIP-STRUCTFAST Automated Comparative Modeling (require login account) online
WHAT IF Homology modeling online
RaptorX Threading online
3D-PSSM Threading (it is now Phyre2) online
GenTHREADER Threading. (The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location). mGenTHREADER GenTHREADER online
MUSTER Threading. MUSTER (MUlti-Sources ThreadER) is a new protein threading algorithm to identify the template structures from the PDB library online
SPARKSx SPARKSx / SP series - Threading online
SUPERFAMILY Threading. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,478 completely sequenced genomes against the hidden Markov models online
WebRASP A server for computing energy scores to assess the accuracy and stability of RNA 3D structures online
SETTER SETTER: web server for RNA structure comparison online
PRD A protein-RNA interaction database. Currently, over 10,000 interactions have been stored database
LOOPP A fold recognition program based on the collection of numerous signals, merging them into a single score, and generating atomic coordinates based on an alignment into a homologue template structure online
EBI Numerous services in bioinformatics and chemoinformatics at EBI online
PMP Protein Model Portal. It gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment online
ResProx Resolution-by-proxy or Res(p) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input online
PSI Protein model portal: interactive modeling online
ProModel ProModel is a complete package for modeling proteins (standalone, linux, windows) standalone
GPCRM Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. GPCR structure predictor incorporating two distinct loop modeling techniques: Modeller and Rosetta server and database
wwPDB Chemical annotation of small and peptide-like molecules at the Protein Data Bank (maintain a single PDB archive of macromolecular structural data) online
Dali The Dali server is a network service for comparing protein structures in 3D online, structural analysis, compare structures
Sysimm Structure and Function Prediction Pipeline Server .
Phyre2 Protein Homology/analogY Recognition Engine .
MUFOLD MUFOLD-Server Protein structure prediction .
chunk-TASSER A protein structure prediction method that combines threading templates from SP3 and ab initio folded chunk structures (three consecutive segments of regular secondary structures). It is better for extreme hard targets .
BioSerf BioSerf v2.0 (Automated Homology Modelling), also, Psipred, FFPred v2.0 (Eukaryotic Function Prediction) .
EVfold Protein Structure Prediction From Sequence Variation .
ASTRO-FOLD version 2.0: an Enhanced Framework for Protein Structure Prediction see article
Foldit Modeling tool .
Foldit The Foldit software provides a natural, intuitive interface to the Rosetta molecular modeling software standalone
GalaxyTBM Protein structure prediction by GalaxyTBM .
MULTICOM An Accurate Multi-Template Comparative Modeling Server for Protein 3D Structure Prediction .
Scratch Protein predictor .
TASSER-VMT Protein Structure Prediction tool .
(PS)2 Protein Structure Prediction Server online
MESHI A software package for protein modeling .
IntFOLD The IntFOLD Integrated Protein Structure and Function Prediction Server online
nFOLD The nFOLD3 Protein Fold Recognition Server online
Glycan Glycan fragment database: a database of PDB-based glycan 3D structures database, structural analysis
MORPHEUS MORPHEUS is a tool to identify and rebuild residues in predicted models with a large error standalone
PSS Protein Structural Statistics. PSS reads an ensemble of PDB files of protein structures, performs a multiple sequence alignment, and computes structural statistics for each position of the alignment standalone
PconsD A fast, stream-computing method for distance-driven model quality assessment standalone
ThreaDom Extracting protein domain boundary information from multiple threading alignments standalone
FFAS The Fold and Function Assignment System online
LINK Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility online, structural analysis
CD-HIT  Widely used program for clustering and comparing protein or nucleotide sequences (see also the standalone version) online, sequence clustering
CAPITO A web server-based analysis and plotting tool for circular dichroism data online
EvoDesign De novo protein design based on structural and evolutionary profiles online
eVolver Optimization of synthetic protein sequences to stabilize the respective structures online and standalone
T-RMSD Web server for automated fine-grained protein structural classification online
CABS-fold Server for the de novo and consensus-based prediction of protein structure online
eThread Template-based protein structure prediction using meta-threading and machine learning online and standalone
eGenome Database: provides an easy access to the results of the large-scale modeling of structures and functions of gene products across entire proteomes online
GeneSilico  Metaserver: This is a gateway to various methods for protein structure prediction online
Protinfo ABCM Protein structure prediction online
PIGS PIGS Server (Prediction of Immuno Globulin Structure) online, nice logo with the head of 3 cute little pigs surrounding an Ab
HHpred  Homology detection & structure prediction by HMM-HMM comparison online
PSiFR  Protein Structure and Function prediction Resource online
EsyPred3D  Homology modeling (you can easily select your template) online
GPCR-ITASSER  Homology modeling for GPCR online
LINK GPCR modeling and simulation toolkit online
GPCR-SSFE  homology modeling for GPCR online
LINK RosettaAntibody online
LINK If you need for instance a protein sequence (of course you will have to guess what type of name you will have to give, unless you know by heart some access numbers, you can use Prosite at the Expasy web site online
LINK If you need straight to the point sequence alignment, you can check at this web page online
LINK Make sequence file from PDB file (sequence from PDB file) online
CBS CBS prediction servers - Numerous tools to analyze protein sequences, Post-translational modifications of proteins, Protein function and structure:  ChloroP LipoP NetNES SecretomeP SignalP, TargetP TatP DictyOGlyc NetAcet NetCGlyc NetCorona NetGlycate NetNGlyc NetOGlyc NetPhorest NetPhos NetPhosBac NetPhosK NetPhosYeast NetPicoRNA NetworKIN, ProP, YinOYang , distanceP, EPipe (Functional differences of protein variants), InterMap3D, NetSurfP, NetTurnP , ProtFun, RedHom (Reduction of sequence similarity in a data set), TMHMM, VarDom Glycosylation and many other tools online
NetOglyc The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins Glycosylation, online
GlycoPP  Webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s) Structural bioinformatics Glycosylation, online
GlyProt  Performs an in silico glycosylation of proteins. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II Structural bioinformatics Glycosylation, online
LINK The Uppsala Electron Density Server: check your favorite experimental Xray structure Protein X-ray structural analysis
VHELIBS VHELIBS is an open source software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed Standalone
LINK SeqAlert(c) is a sequence alerting service that will periodically compare your sequence(s) against sequences from determined 3D structures, or structures being determined ... Information about the 3d structure you are waiting for
FoldIndex  Tries to answer to the question: Will this protein fold? Structural Analysis, folding online
PROFcon The PROFcon server uses neural network method that utilizes sequence information, secondary structure and solvent accessibility predictions, and the overall properties of the entire protein to predict residue contacts standalone
CORNET The CORNET server is a neural network based predictor that uses as input correlated mutations, sequence conservation, predicted secondary structure and evolutionary information Analysis of the quality of the 3D structure online
Swissmodel Homology modeling online
Robetta Homology modeling online
I-TASSER Homology modeling online
QUARK  Internet service for ab initio protein folding and protein structure prediction online
IntFOLD Integrated Protein Structure and Function Prediction Server online
GPCRautomodel Homology modeling online
LOMETS Local Meta-Threading-Server. web service for protein structure prediction online
3djigsaw This server builds three-dimensional models for proteins based on homologues of known structure online
BSR BSR Binding Site Refinement employs a new template-based method for the local refinement of ligand-binding regions in protein models using closely as well as distantly related templates identified by threading online
Memoir Template-based structure prediction for membrane proteins online
LINK Links to Macromolecular structures in 3D Databases of Macromolecules in 3D, online
PDB The Protein Data Bank 3D structure database online
ENTREZ The Entrez Structure Database Macromolecule database online
PDBCat  Can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc. Tools to manipulate PDB files, standalone
LINK Atlas of protein side-chain interactions within known protein structures and interactions with DNA Macromolecule interaction database, online
Glyco     Glycoconjugate Data Bank: Structures and annotated glycan structure database and N-glycan primary structure verification service online
LINK Many structural bioinformatics tools Tools to analyze macromolecules online
LINK Many tools for structural bioinformatics, loop prediction, simulation, structural refinement of proteins with Gromacs, Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent, small molecules Structural bioinformatics online
Bodil  Biomolecular modeling package Molecular modeling standalone
GalaxyWEB GalaxyWEB server for protein structure prediction and refinement online
MaxSprout MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace online
Seq2Struct Seq2Struct, a web resource for the identification of sequence-structure links online
ModWeb A Server for Protein Structure Modeling with Modeller (passwd required) online
ModPipe  A completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention online
Modeller Modeller: software package for homology or comparative modeling of protein 3D structures Homology modeling, standalone
Jackal Protein structure modeling package Homology modeling, loop prediction related tools, standalone
PSIPRED PSIPRED web servers performing secondary structure prediction, transmembrane topology prediction or protein fold recognition Protein structure prediction online
LINK CG database, membrane proteins database online
PDBTM Protein Data Bank of Transmembrane Proteins database online
LINK The GPCR modeling and simulation toolkit. This web server is developed by the Structural Bioinformatics group at the Public Galician Foundation of Genomic Medicine, University Hospital of Santiago de Compostela GPCR online
BinMemPredict A web server and software for predicting membrane protein types Protein membrane online
LINK OPM database and PPM web server: resources for positioning of proteins in membranes Protein membrane online
PredictProtein Webserver for homology modeling and protein function prediction Homology modeling related tools online
Robetta Web server for protein structure prediction and analysis Protein structure prediction online
SPACE SPACE server includes tools for predicting and analyzing structures of biomolecules and their complexes online
SABBAC SABBAC: online structural alphabet-based protein backbone reconstruction from alpha-carbon trace Protein structure prediction
PS2 Protein structure prediction server: automated homology modeling server using a consensus strategy between psi-blast, impala and T-coffee with a final 3D structure modeled with Modeller Homology modeling, related tools online
RosettaDesign Server for identifying low energy amino acid sequences from the backbone coordinates of the target structure Protein structure prediction onine
ModBase ModBase: Database of Comparative Protein Structure Models. Currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences database of homology models
ESPript ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences Protein structure prediction, sequences, standalone
RaptorX  A new protein structure prediction program, Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions. RaptorX also assigns the following confidence scores to indicate the quality of a predicted 3D model online, got very good results at CASP9 for instance
CPHmodels CPHmodels 3.2 Server homology modeling server at DTU online
ADP_EM Fast exhaustive multi-resolution docking for high-throughput coverage. This novel method makes it possible to accurately dock atomic structures into low-resolution electron-density maps Docking modules into low resolution electron-density maps, can help for homology modeling of large structures