- APBS (Adaptive Poisson-Boltzmann Solver): evaluating the electrostatic properties of biomolecules.
- Atlas of protein side-chain interactions.
- CaPTURE, cation-pi interaction analysis
- castP: A Server for Identification of Protein Pockets & Cavities
- Comparer, multiple structure aligment, outputs sequence aligment.
- ConSurf server: identification of functional regions in proteins
- DALI (3-D structure database searches) and Dali Lite (Pairwise comparison of protein structures)
- 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.
- ESCET: analysis and comparison of 3D protein structures by T. Schneider.
- Evolutionary Trace Server
- GROMACS: molecular dynamics.
- HBexplore: analysis of hydrogen bonds in macromolecules.
- 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.
- 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.
- PRODRG Server-Dundee
- PROPKA, empirical prediction and interpretation of protein pKa values
- ProMate, prediction of potential binding sites
- Protein-Protein Interaction Server
- 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 ).
- SURFNET : Surfaces, cavities, etc.
- TOPS : protein topology cartoons (EBI)
- Uppsala Software Factory (USF).
- Structural alignment :
- CE-MC: Multiple Protein Structure Alignment Server (Univ Albany)
- Dali Lite (Pairwise comparison of protein structures)
- MAPS : Multiple Alignment of Protein Structures
(access via Web Server).
- MUSTANG Multiple Strutural Alginment Algorithm (Alternative site).
- RAPIDO: Rapid Alignment of Protein structures In the presence of Domain mOvements
- Stralign: Structure alignment for 3D protein structures.
- STRAP: Multiple sequence and structure alignment.
- TCoffee, includes Expresse 3D alignment
- Theseus, maximum likelihood superpositioning and analysis of macromolecular structures.
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