Structure databases |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
- 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.
- BANΔIT, normalized B-factor analysis and ΔB' interpretation server.
- CaPTURE, cation-pi interaction analysis
- castP: A Server for Identification of Protein Pockets & Cavities
- CAVER: analysis and visualization of tunnels and channels in proteins.
- 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.
- Metal Sites :
- NACCESS Atomic Solvent Accessible Area Calculations.
- PARVATI : Protein Anisotropic Refinement Validation and Analysis
- PDBrenum: renumbering of residues in PDB files with UniProt numbering.
- 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).
- Structuprint: 2D representation of protein structures' surfaces.
- 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), since 2019 also in GitHub.
- WebFEATURE: Automated function prediction in protein structures.
- Structural alignment and comparison :
- 3d-SS: 3-Dimensional Structural Superposition
- CE-MC: Multiple Protein Structure Alignment Server (Univ Albany)
- Dali Lite (Pairwise comparison of protein structures)
- ENSEMBLATOR: create ensembles from pdb files, and compare those ensembles.
- Foldseek: fast and accurate protein structure search.
- MUSTANG Multiple Strutural Alginment Algorithm (Alternative site).
- POSA: user-driven, interactive multiple protein structure alignment server.
- Profit: least squares fitting.
- RAPIDO: Rapid Alignment of Protein structures In the presence of Domain mOvements
- SALIGN: multiple protein sequence/structure alignment server.
- 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.
- US-align: Universal Structural alignment of macromolecules.
- Binding sites and pockets :
|
|
|
|
|
|
|
|
- BioSync, A Structural Biologist's Guide to Synchrotron Facilities
- Lightsources.org: information and updates about light sources.
- EUROPE
- AMERICA
|
|
|
|
|
|
|
|
|
|