3D structure utilities

 

  • SANSparallel - Interactive homology search against Uniprot. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT.It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest (2015) - online
  • Omokage - Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB (2016) - online
  • Solvate - Construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations - standalone
  • AcquaAlta - A directional approach to the solvation of ligand-protein complexes (water molecules between protein and ligand, hydrate, solvate) - online
  • PISCES - The tool has several capabilities in producing subsets of sequences from larger data sets (collect proteins with a given % of sequence identity/similarity - online
  • PhyloBot - Phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function (runs on elastic cloud computing resources from Amazon Web Services) - online
  • ProTSAV - A protein tertiary structure analysis and validation server - online
  • locPREFMD - Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD - online
  • ProQ2 - Estimation of model accuracy implemented in Rosetta - standalone
  • conSSert - Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure - online
  • Qprob - Protein single-model quality assessment by feature-based probability density functions - online
  • RaptorX - RaptorX Property is a web server predicting structure property of a protein sequence without using any templates - online
  • PHYLOViZ - Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees - online
  • Evolview - Version 2. Online visualization and management tool for customized and annotated phylogenetic trees - online
  • SL2 - SuperLooper2 is the updated of SuperLooper, a fragment based tool for the prediction and interactive placement of loop structures into globular and helical membrane proteins - online
  • MPI - The MPI Bioinformatics Toolkit: Open, interactive web service for comprehensive and collaborative protein bioinformatic analysis - online
  • DNATCO - Assignment of DNA conformers - online
  • BetaSCPWeb - Side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization - online
  • FoXSDock - Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles (FoXS, FoXSDock and MultiFoXS) - online
  • NAPS - Network Analysis of Protein Structures - online
  • LassoProt - The server collects information about proteins and other (bio)polymers with lassos. LassoProt detects loops (closed by cysteine, as well as amide, ester, thioester and other bridges) in a given (bio)polymer, determines surfaces of minimal area spanned on such loops, and analyzes if and how termini of the polymer intersect these minimal surfaces… - online
  • ALVIS - Sequence Bundles is a new method for visualising sequence alignments - online
  • ProViz - Web-based visualization tool to investigate the functional and evolutionary features of protein sequences - online
  • RaptorX-Property - Protein structure property prediction (input sequence) - online
  • PhyreStorm - A Web Server for Fast Structural Searches Against the PDB - online
  • Cloud4Psi - Cloud Computing for 3D Protein Structure Similarity Searching - standalone
  • DbD - Disulfide (bond) by Design using 3D data - online
  • itol - Interactive Tree Of Life: an online tool for the display and manipulation of phylogenetic trees - online
  • Cyscon - Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins - online
  • Omokage - Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) - online
  • NMRe - A web server for NMR protein structure refinement with high-quality structure validation scores - online
  • Fit3D - A bioinformatics web service to search for spatial residue patterns in proteins, so-called structural motifs - online
  • SMART - Simple Modular Architecture Research Tool is a web resource providing simple identification and extensive annotation of protein domains and the exploration of protein domain architectures - online
  • ProteomeScout - A repository and analysis resource for post-translational modifications and proteins - online
  • MODIP - Modeling disulphide bonds in Proteins - online
  • MESSA - MEta Sever for Sequence Analysis - online
  • CD spectra - Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy (server) - online
  • ProtDCal - A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins - online and standalone
  • IBS - An illustrator for the presentation and visualization of biological sequences - online and standalone
  • INGA - Protein function prediction combining interaction networks, domain assignments and sequence similarity (2015) - online
  • TOPCONS - The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides (2015) - online
  • PhyloGene - Server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles (2015) - online
  • SIFTER - A web server for accurate phylogeny-based protein function prediction (2015) - online
  • CATH - CATH FunFHMMer web server: protein functional annotations using functional family assignments (2015) - online
  • Proteus - Computational protein design. The software allows positive and negative design - standalone
  • cellPACK - cellPACK is a software program that extends autoPACK with biologically relevant packing algorithms and a database of molecular recipes to construct models of whole cells or viruses - standalone
  • Compadre - Using homology relations within a database markedly boosts protein sequence similarity search (2015) - online
  • PROCAIN - Server for remote protein sequence similarity search (2009) - online
  • SEQATOMS - A web tool for identifying missing regions in PDB in sequence context - online
  • BCSearch - Fast structural fragment mining over large collections of protein structures - online
  • Link - CATH FunFHMMer web server: protein functional annotations using functional family assignments - online
  • CCTOP - Given the amino acid sequence of a putative α-helical transmembrane protein, CCTOP predicts its topology - online
  • Skylign - A tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models. Profile can be found via Pfam and or generated with HMMER - online
  • VAST+ - Tracking structural similarities between macromolecular complexes - online
  • HMMER - It is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs) - online
  • iPfam - The iPfam database is a catalog of protein family interactions, including domain and ligand interactions, calculated from known structures - database
  • CSandS - Coding Sequence and Structure database provides a comprehensive mapping between solved protein structures and the genomic sequences that encode them (Synonymous codon usage influences the local protein structure observed) - database
  • LocSigDB - It is a manually curated database of experimental protein localization signals for eight distinct subcellular locations - database
  • JPred4 - Aprotein secondary structure prediction server. JPred4 features higher accuracy, with a blind three-state (helix, strand, coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible - online
  • TCS - A web server for multiple sequence alignment evaluation and phylogenetic reconstruction - online
  • MarkUs - A server to navigate sequence-structure-function space - online
  • CDvist - A webserver for identification and visualization of conserved domains in protein sequences - online
  • RRDistMaps - A UCSF Chimera tool for viewing and comparing protein distance maps - standalone
  • Chemo tools - Protein Circular Dichroism Data Bank and Tools related to Circular Dichroism - database
  • DNAtools - tools for DNA - online
  • topmatch - Protein structure alignment and visualization of structural similarities - online
  • MATRAS - A web server for comparing protein 3D structures - online
  • BioSuper - A web tool for the superimposition of biomolecules and assemblies with rotational symmetry - online
  • MODA - Membrane optimal docking area. A tool to predict online potential membrane binding site on a protein 3D structure - online
  • GlycoSuiteDB - Unicarbkb provides information on both the glycan structure and glycosylated peptides of proteins - online
  • PyWATER - A PyMOL plug-in to find conserved water molecules in proteins by clustering - standalone
  • MobyWat - Mobility-based prediction of hydration structures of protein surfaces - standalone
  • ccSol - Sequence-based prediction of protein solubility - online
  • ESPRESSO - EStimation of PRotein ExpreSsion and SOlubility is a sequence-based predictor for estimating protein expression and solubility - online
  • TMDET - Detection of transmembrane regions by using 3D structure of proteins - online
  • GlycomeDB - Carbohyrate data from CFG , KEGG, BCSDB, Carbbank - database
  • GlycoBase - Glycan structures - database
  • GlycoProtDB - GPDB - database
  • CFG - Consortium Functional Glycomics glycan structure database. CFG provides one of the largest databases for understanding the roles of carbohydrates in cell communication
  • EuroCarbDB - GlycanBuilder and many others - online
  • Databases - A series of PDB-related databanks for everyday needs. HSSP, PDBREPORT and PDB_REDO...The BDB databank holds X-ray PDB files with consistently represented B-factors - database
  • ValidatorDb - A database of validation results for all residues and ligands from the Protein Data Bank - database
  • Validator - MotiveValidator: Validate ligand and residue structure in biomolecular complexes - online
  • Alignment - Alignment-Annotator: Rendering and annotating sequence alignments - online
  • Alignment - Alignment-Annotator: Rendering and annotating sequence alignments - online
  • LocTree3 - Prediction of localization (prediction of protein sub-cellular localization) - online
  • AIDA - Ab initio domain assembly server - online
  • POSA - A user-driven, interactive multiple protein structure alignment server (Partial Order Structure Alignment) - online
  • ESBRI - Evaluating the Salt BRIdges in Proteins - online
  • ESPript - ESPript 3 (renders sequence similarities and secondary structure information from aligned sequences for analysis and publication purpose) - online
  • ENDscript - ENDscript 2 (ENDscript is a friendly Web server, which extracts and renders a comprehensive analysis of primary to quaternary protein structure information in an automated way) - online
  • Peeling - Protein Peeling 3 D: Splitting a protein structure into proteins units and domains - online
  • GlobPlot - Intrinsic Protein Disorder, Domain & Globularity Prediction - online
  • DSDBASE - DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein - database
  • DISULFIND - Cysteines Disulfide Bonding State and Connectivity Predictor - online
  • SABLE - Accurate sequence-based prediction of relative Solvent AccessiBiLitiEs - online
  • SURF's_UP - A web tool for analysis of functional relationships in protein families as inferred from protein surface maps comparison - online
  • FunClust - FunClust is a web server for the identification of local functional motifs in a set of non homologous protein structures. You can submit a set of protein structures deemed to share a common function (e. g. they bind similar ligands, interact with similar protein interfaces or share an enzymatic activity) - online
  • DHcL - Domain Hierarchy and closed Loops is a server for the analysis of basic structural units of a protein. The server calculates domain structures at different levels of energy hierarchy and elements of the loop-n-lock structure, closed loops and van der Waals locks - online
  • Pratt - The Pratt pattern finder program is able to discover patterns conserved in sets of unaligned protein sequences. The output is in the form of Prosite patterns - online
  • CAZy - The Carbohydrate-Active Enzymes database provides online and continuously updated access to a sequence-based family classification Linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides - database
  • WATsite - WATsite identifies hydration sites from a molecular dynamics simulation trajectory and predicts the free energy profile of each hydration site. The results of WATsite can be displayed in PyMOL and be used to estimate the protein desolvation free energies for any bound or docked ligand - standalone
  • Translate - Gene to amino acid sequence - online
  • RaptorX-SS8 - Secondary structure prediction - online
  • Meta-PP - Secondary structure prediction - online
  • BION - BION web server: Predicting non-specifically bound surface ions - online
  • VIPERdb - Virus particle exploreR. A database for icosahedral virus capsid structures - database
  • mmtsb - Multiscale Modeling Tools for Structural Biology. Protein modeling, nucleic acid modeling - standalone
  • PDB_hydro - Point mutation, loop prediction, solvation, place waters, solvate with AQUASOL - online
  • translate - Gene to amino acid sequence - online
  • PREDATOR - Secondary structure prediction - online
  • YASSPP - Secondary structure prediction - online
  • PSSpred - Secondary structure prediction - online
  • PSSpred - Transmembrane helix prediction - online
  • Phobius - Transmembrane helix prediction - online
  • PHDhtm - Transmembrane helix prediction - online
  • MEMSAT - (via PSIPRED) Transmembrane helix prediction - online
  • HMMTOP - Transmembrane helix prediction - online
  • SCWRL4 - Improved prediction of protein side-chain conformations with SCWRL4 - standalone
  • PROMALS3D - Constructs 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 - online
  • RASP - RApid Side-chain Predictor - standalone
  • CISRR - CISRR is a user friendly program for accurate prediction of protein side chains and effective elimination of their inner atomic clashes - standalone
  • dDFIRE - dDFIRE/DFIRE2: Energy calculation - online
  • PREDDIMER - PREDDIMER: a web server for prediction of transmembrane helical dimers - online
  • PROTEAND - PROTEAND generates interactive graphical representations that highlight uncertainty in atomic coordinates - standalone
  • PDBFixer - PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them - standalone
  • MAFFT - Multiple sequence alignment and NJ / UPGMA phylogeny - online
  • ClustalW2... - Multiple Sequence Alignment: ClustalW2, Kalign, MAFFT... at EBI - online and standalone
  • MUSCLE - Multiple alignment - standalone
  • PFP - PFP: Automated Protein Function Prediction: PFP algorithm extracts function information (GO terms) from sequences retrieved by PSI-BLAST - online
  • Needleman - Needleman-Wunsch algorithm: Protein sequence similarity - online
  • ESG - The Extended Similarity Group (ESG) Algorithm. ESG runs PSI-BLAST iteratively and advocates functional terms that occur consistently in the series of PSI-BLAST database searches - online
  • FPSPD - The Functional Protein Sequence Pattern Database (FPSPD) is a fully automated database of protein sequences patterns derived from the analysis of the conserved residues that are predicted to be functional in structurally-aligned homologous families in the HOMSTRAD database - standalone
  • Bioinfo - Bioinformatics Tools for protein structure analysis, and evaluation, renumber PDB file, rename chain in PDB file online...membrane helix prediction, compute HBPLUS H-bonds, evaluate models with VALPRED 3D - online
  • UniProt - High-quality and freely accessible resource of protein sequences and functional annotation - online
  • Gene3D - A database of protein domain structure annotations for protein sequences - online
  • SCOP2 - SCOP2 is a successor to the Structural Classification of Proteins (SCOP) database - online
  • SIMAP - The Similarity Matrix of Proteins database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics - online
  • MP:PD - The membrane protein packing database is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters - online
  • RING - A web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with CYTOSCAPE - online
  • CAMEO - Continuously evaluate the accuracy and reliability of predictions (protein and binding site) - .
  • TIGRESS - Princeton_Tigress: Using this protocol, one can consistently refine a prediction to help bridge the gap between a predicted structure and the actual native structure - online
  • GOAP - A generalized orientation-dependent, all-atom statistical potential for protein structure prediction. It was benchmarked against other state-the-art similar potentials and was shown to be significantly better for discriminating native structures from decoys. Protein structure quality assessment - Standalone
  • KoBaMIN - A Knowledge Based MINimization Web Server for Protein Structure Refinement - online
  • BCL::Fold - De novo prediction of large proteins by assembly of secondary structure elements - standalone
  • UNRES - A package to carry out coarse-grained simulations of protein structure and dynamics - standalone
  • Evolver - ProteinEvolver: Generates samples of protein-coding genes and protein sequences evolved along phylogenies under structure-based substitution models. These models consider the protein structure to evaluate candidate mutations, which can be accepted (substitutions) or rejected depending on the energy of the protein structure of the mutated sequence - standalone
  • MAMMOTH - Matching Molecular Models Obtained from Theory is a sequence-independent protein structural alignment method. It allows the comparison of an experimental protein structure with an arbitrary low-resolution protein tertiary model. It also allows the comparison of two experimental structures, or the search for similar structures to a query structure in a database - standalone
  • PROMIS - The Promis Server: Enzyme promiscuity prediction - online
  • Dali - The Dali server is a network service for comparing protein structures in 3D - online, structural analysis, compare structures
  • Glycan - Glycan fragment database: a database of PDB-based glycan 3D structures - database
  • MORPHEUS - MORPHEUS is a tool to identify and rebuild residues in predicted models with a large error - standalone
  • PSS - 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. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles - 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
  • Link - EMBOSS is The European Molecular Biology Open Software Suite. Popular applications include: prophet Gapped alignment for profiles; infoseq Displays some simple information about sequences; water Smith-Waterman local alignment; pepstats Protein statistics; showfeat Show features of a sequence; palindrome Looks for inverted repeats in a nucleotide sequence; eprimer3 Picks PCR primers and hybridization oligos; profit Scan a sequence or database with a matrix or profile; extractseq Extract regions from a sequence; marscan Finds MAR/SAR sites in nucleic sequences; tfscan Scans DNA sequences for transcription factors; patmatmotifs Compares a protein sequence to the PROSITE motif database; showdb Displays information on the currently available databases; wossname Finds programs by keywords in their one-line documentation; abiview Reads ABI file and display the trace; tranalign Align nucleic coding regions given the aligned proteins - online and standalone
  • Link - The Fold and Function Assignment System (FFAS) server - online, structural analysis
  • Link - Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility - online, structural analysis
  • Link - CD-HIT is a widely used program for clustering and comparing protein or nucleotide sequences (see also the standalone version) - online, sequence clustering
  • Link - CAPITO: a web server-based analysis and plotting tool for circular dichroism data - online
  • Link - EvoDesign: de novo protein design based on structural and evolutionary profiles - online
  • Link - eVolver: Optimization of synthetic protein sequences to stabilize the respective structures - online and standalone
  • Link - T-RMSD: a web server for automated fine-grained protein structural classification - online
  • Link - ValiDichro: a website for validating and quality control of protein circular dichroism spectra - online
  • Link - DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale - online
  • Link - eGenome database: provides an easy access to the results of the large-scale modeling of structures and functions of gene products across entire proteomes - database
  • Link - HMMER web server: interactive sequence similarity searching - online
  • Link - mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet - online
  • Link - The Voronoi Laguerre Delaunay Protein web server (VLDPws): a geometric tool for analyzing protein structures in their environment - online
  • Link - Supercharge refers to increasing the net charge of a protein by mutating surface residues. Increasing net charge can improve reversibility of unfolding by preventing aggregation of partially unfolded states - online, avoid protein aggregation
  • Link - SwissSidechain: a molecular and structural database of non-natural aa sidechains (for peptides and proteins) - database
  • Link - foXs: Fast SAXS Profile Computation with Debye Formula - online
  • Link - Mark-Us: A Function Annotation Server for Protein Structures - online
  • Link - RCSB PDB - jCE/jFATCAT Structure Alignment Server : All vs All Protein Structure Comparison and Alignment - online
  • Link - GeneSilico Metaserver: This is a gateway to various methods for protein structure prediction - online
  • Link - PINALOG: a novel approach to align protein interaction networks, implications for complex detection and function prediction - online
  • Link - CombFunc: predicting protein function using heterogeneous data sources. The CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions - online
  • Link - HH-suite sequence alignments - standalone
  • Link - HH-suite sequence alignments, with the other tools - online
  • Link - HHfrag: HMM-based fragment detection using HHpred - online
  • Link - SAFrag 1.0 Efficient candidate fragment search from amino acid sequence - online
  • Link - PIGS Server (Prediction of Immuno Globulin Structure) - online, nice logo with the head of 3 cute little pigs surrounding an Ab
  • Link - pKNOT v.2: the protein KNOT web server - online
  • Link - COFACTOR: an accurate comparative algorithm for structure-based protein function annotation - online
  • Link - HHpred - Homology detection & structure prediction by HMM-HMM comparison - 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 - If you need to align 2 sequences and get simple sequence identity and similarity, you can try at: StretcherN. As usual, you will need to get things in Fasta format while a simple texte file could do it equally well, but, no - online
  • Link - Make sequence file from PDB file (sequence from PDB file) - online
  • UniCarbKB - Offers public access to a growing, curated database of information on the glycan structures of glycoproteins - online
  • Link - The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins - Glycosylation, online
  • Link - GlycoPP is a webserver for predicting potential N-and O-glycosites in prokaryotic protein sequence(s) - Structural bioinformatics Glycosylation, online
  • Link - 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
  • Link - 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
  • Link - FoldIndex tries to answer to the question: Will this protein fold? - Structural Analysis, folding online
  • Link - 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
  • Link - 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
  • Link - Atlas of Side-Chain and Main-Chain Hydrogen Bonding, it gives values - Training - introduction
  • Link - GANGSTA+ is a non-sequential structure-alignment tool, compare the structure of a protein with more than 10,000 others. Compare the structures of a pair of proteins and perform a sequence scoring - Structural bioinformatics online
  • Link - Biskit is a modular, object-oriented Python library for structural bioinformatics research - Python library for structural bioinformatics research, standalone
  • Link - 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
  • Link - Links to Macromolecular structures in 3D - Databases of Macromolecules in 3D,
  • Link - The Protein Data Bank - 3D structure database
  • Link - The Entrez Structure Database - Macromolecule database
  • Link - 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
  • Link - Glycoconjugate Data Bank: Structures and annotated glycan structure database and N-glycan primary structure verification service - database
  • 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
  • Link - SCWRL 4 is the most recent version of the SCWRL program for prediction of protein side-chain conformations - Predict protein side chain conformation
  • Link - GalaxyWEB server for protein structure prediction and refinement - online
  • Link - DOMpro is a web server to predict protein domain boundaries - online, domain prediction
  • Link - CDD server: Search for Conserved Domains within a protein sequence - online, domain prediction
  • Link - MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace - online
  • Link - Seq2Struct, a web resource for the identification of sequence-structure Links - online
  • Link - CG database, membrane proteins - database
  • Link - PDBTM: Protein Data Bank of Transmembrane Proteins - database
  • Link - Pred-TMBB: web server for predicting the topology of beta-barrel outer membrane proteins - Protein structure prediction online
  • Link - ProteinDBS: web server for detection of similar protein tertiary structures - Protein structure analysis, Structural similarity search, online
  • Link - FATCAT: web server for flexible structure comparison and structure similarity searching - Protein structure analysis, Structural similarity search online
  • Link - PREDITOR: Program for predicting dihedral angles from chemical shifts and/or sequential homology - Protein structure determination online
  • Link - SABBAC: online structural alphabet-based protein backbone reconstruction from alpha-carbon trace - Protein structure prediction
  • Link - TransFold : web server for predicting the structure and residue contacts of transmembrane beta-barrels - Protein structure prediction online
  • Link - RosettaDesign: Server for identifying low energy amino acid sequences from the backbone coordinates of the target structure - Protein structure prediction onine
  • Link - iSee: iSee is an intuitive and interactive approach for the dissemination of structural biology data - Protein structure analysis, annotation, standalone
  • Link - TarO analyses a protein sequence by a large number of bioinformatics techniques - online
  • Link - The Jpred 3 secondary structure prediction server. A Secondary Structure Prediction Server - Protein structure prediction online
  • Link - ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences - Protein structure prediction, sequences, standalone
  • Link - 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 - standalone
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira