Structural Biology tools

(Inspired from Pereda's Lab)

Crystallizability predictors :)

Structure databases

Structure solution and refinement

Model building

Structure validation (and related)

Molecular Graphics

Structure analysis
  • Electrostatic properties :
    • APBS (Adaptive Poisson-Boltzmann Solver): evaluating the electrostatic properties of biomolecules.
    • Bluues: Electrostatic properties of proteins based on generalized Born radii.
    • DelPhi: A Finite Difference Poisson-Boltzmann Solver (DelPhi Web Server).
    • PIPSA: comparison of the electrostatic interaction properties of proteins.
    • PROPKA, empirical prediction and interpretation of protein pKa values
  • Atlas of protein side-chain interactions.
  • CaPTURE, cation-pi interaction analysis
  • castP: A Server for Identification of Protein Pockets & Cavities
  • COLORADO3D: server for the visual analysis of protein structures, includes sequence conservation coloring.
  • ConSurf server: identification of functional regions in proteins
  • DALI (3-D structure database searches) and Dali Lite (Pairwise comparison of protein structures)
  • Disulfide by design: design of disulfide bonds.
  • 3DNA analysis, rebuilding and visualization of nucleic acid structures.
  • Dynamite: web-server that predicts protein motions.
  • DynDom, Protein domain motion analysis.
  • elNEMO: computes the low frequency normal modes of a protein, with potential use in difficult molrep problems.
  • ESBRI: evaluation of salt bridges in proteins.
  • ESCET: analysis and comparison of 3D protein structures by T. Schneider.
  • Evolutionary Trace Server (Lichtarge Lab)
  • GROMACS: molecular dynamics.
  • HBexplore: analysis of hydrogen bonds in macromolecules.
  • HOLE: analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.
  • Indonesia : integrated program package for biological sequence analysis. Includes Structure-based multiple sequence alignment.
  • Interhlx : interhelical angles calculation. 
  • LigPlot : schematic diagrams of protein-ligand interactions. 
  • Mark-Us: A Function Annotation Server for Protein Structures.
  • MESPEUS database: Metal Sites in Proteins.
  • NACCESS Atomic Solvent Accessible Area Calculations.
  • PARVATI : Protein Anisotropic Refinement Validation and Analysis
  • PINTS: Patterns in Non-homologous Tertiary Structure
  • PiQSi: Protein quaternary structure investigation.
  • PISA: Protein Interfaces, Surfaces and Assemblies.
  • PLATINUM: Calculation and visualization of molecular hydrophobic/hydrophilic properties.
  • PRODRG Server-Dundee
  • ProMate, prediction of potential binding sites
  • Protein Geometry Database
  • 2P2Idb: Protein-protein interaction analysis, drugability and inhibitiors.
  • Protein-Protein Interaction Server, new server at Sussex
  • Pro-Origami: Protein Structure Cartoons.
  • ProtSkin, converts a protein sequence alignment to a property file used to map the sequence conservation onto the structure.
  • RAPPER server: ab initio conformational search algorithm for restraint-based protein modelling.
  • SPASM server, recognition of spatial motifs (Uppsala Software Factory).
  • SSBOND: Model building of disulfide bonds (Bart Hazes)
  • Structural Thermodynamics Calculations, free energy calculations from the structure of different complexes.
  • STructure ANalysis server (Uppsala Software Factory).
  • Surface Racer, calculation of accessible surface area, molecular surface area and average curvature of molecular surface, also analyses of cavities in the protein interior.
  • SURFNET : Surfaces, cavities, etc. 
  • TOPS : Topology of Protein Structure
  • Uppsala Software Factory (USF).
  • WebFEATURE: Automated function prediction in protein structures.
  • Structural alignment :
    • 3d-SS: 3-Dimensional Structural Superposition
    • CE-MC: Multiple Protein Structure Alignment Server (Univ Albany)
    • Dali Lite (Pairwise comparison of protein structures)
    • MUSTANG Multiple Strutural Alginment Algorithm (Alternative site).
    • Profit: least squares fitting.
    • RAPIDO: Rapid Alignment of Protein structures In the presence of Domain mOvements
    • STAMP: structural alignment of multiple proteins (Barton group).
    • Stralign: Structure alignment for 3D protein structures.
    • STRAP: Multiple sequence and structure alignment.
    • TCoffee, includes Expresso 3D alignment
    • Theseus, maximum likelihood superpositioning and analysis of macromolecular structures.
  • Binding sites and pockets :
    • DoGSiteScorer: Active Site Prediction and Analysis Server
    • FTsite binding site prediction (Structural Bioinformatics group, Univ Boston)
    • fpocket: protein pocket (cavity) detection.
    • GHECOM (Grid-based HECOMi finder): finding multi-scale pockets on protein surfaces.
    • MetaPocket: a meta server to identify ligand binding sites, combines predictions from eight methods.

Crystallization

Teaching and Tables

Synchrotrons

Suppliers: crystallization and related

X-Ray Equipment

SAXS