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URLs 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