3D quality control

  • CREDO - CREDO is a relational database storing all pairwise atomic interactions of inter- as well as intra-molecular contacts between small- and macromolecules found in experimentally-determined structures from the Protein Data Bank (PDB) Structural variations from EnsEMBL Variation are mapped onto all protein structures in CREDO through the sequence-to-structure mapping. EnsEMBL Variation contains variation data from the most important sources, including dbSNP, COSMIC and UniProt as well as information about (disease) phenotypes that can be Linked to variations occurring in protein structures. This means that phenotypes can be Linked directly to ligand binding sites or protein-protein interfaces. Interactions between atoms are stored as Structural Interaction Fingerprints (SIFts) that were described first by Deng et al.. CREDO currently implements 13 different interaction types such as hydrogen bonds, halogen bonds, carbonyl interactions and others - online
  • GalaxyRefine - Protein structure refinement driven by side-chain repacking - online
  • NIAS-Server - Neighbors Influence of Amino Acids and Secondary Structures - online
  • FRST - Energy Validation - online
  • QMEAN - Server for Model Quality Estimation - online
  • Solvx - Structure Validation, Solvation Preference - This server computes the solvation profile for a protein structure. This is useful when assessing the quality of a homology model or an existing PDB structure used in homology modelling. Solvation preference is a measure of solvent accessibility for each residue within a protein; a well-packed structure should have an overall solvation preference below zero. Generally, the more negative this figure is, the better the model - online
  • SAVES - Structural Analysis and Verification Server (Procheck, What_Check, ERRAT, Verify_3D, PROVE, SFCHECK) - online
  • COLORADO-3D - www-tool that greatly facilitates the visual analysis of various features in three-dimensional protein structures, directly at the level of the protein structure, with the aid of commonly used viewers such as RASMOL or SWISSPDBVIEWER. Among the features most important for the structural biologist that our server allows to visualize in color are potential errors in protein structure (detected by ANOLEA, PROSA, PROVE,VERIFY3D), regions buried in the protein core and inaccessible to the solvent, and regions of high or low sequence conservation (e.g. detected by RATE4SITE) - online
  • Map2mod - A server for evaluation of crystallographic models and their agreement with electron density maps - onine
  • VADAR - VADAR (Volume, Area, Dihedral Angle Reporter) is a compilation of more than 15 different algorithms and programs for analyzing and assessing peptide and protein structures from their PDB coordinate data - online
  • SAVS - Stuctural Analysis and Verification Server - online
  • ProQ2 - Model Quality Assessment of Proteins - .
  • RAMPAGE - Structural validation by assessment of the Ramachandran plot (PDB file as input) - standalone
  • APOLLO - Assessing protein single or multiple model(s) - .
  • Dali - The Dali server is a network service for comparing protein structures in 3D - online, structural analysis, compare structures
  • MORPHEUS - MORPHEUS is a tool to identify and rebuild residues in predicted models with a large error - standalone
  • Link - PconsD, a fast, stream-computing method for distance-driven model quality assessment - standalone
  • Link - eVolver - Optimization of synthetic protein sequences to stabilize the respective structures - online and standalone
  • Link - The ModFOLD4 server for the quality assessment of 3D protein models - online
  • Link - VLDP web server - a powerful geometric tool for analysing protein structures in their environment - online
  • Link - QA-RecombineIt - a server for quality assessment and recombination of protein models - online
  • Link - BeEP Server - using evolutionary information for quality assessment of protein structure models - 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 - 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 - 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 - If you need straight to the point sequence alignment, you can check at this web page - 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 - 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 - Structural analysis, Protein Structure, course
  • 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 - Memoir - template-based structure prediction for membrane proteins - online
  • Link - Atlas of protein side-chain interactions within known protein structures and interactions with DNA - Macromolecule interaction database, 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
  • Link - The UCLA-DOE Structure Evaluation server is a tool designed to help in the refinement of crystallographic structures and models - Validate protein structure online
  • Link - ERRAT is a protein structure verification algorithm - Validate protein structure 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 - Robetta - web server for protein structure prediction and analysis - 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 - Harmony - web server for the assessment of protein structures - Protein structure validation online
  • Link - RosettaDesign - Server for identifying low energy amino acid sequences from the backbone coordinates of the target structure - Protein structure prediction onine
  • Link - MolProbity - web server for structure validation and all-atoms contact analysis for nucleic acids and their complexes - Protein structure validation online
  • Link - iSee - iSee is an intuitive and interactive approach for the dissemination of structural biology data - Protein structure analysis, annotation, standalone
  • Last updated on .

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