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
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira