Molecular and Cellular Modeling
HITS gGmbH (formerly EML Research gGmbH), Heidelberg
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2002 -
1988 - 2001
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Tutorials:
COMBINE analysis to derive protein structure-based QSARs
GRID for structure-based drug design
UHBD to compute electrostatic binding free energy
3DFS to do a flexible ligand pharmacophore search
Software:
SYCAMORE: SYstems biology's Computational Analysis and MOdeling Research Environment
RAMD Implementations
AMBER: Patches
NAMD: Scripts
metaPocket2: webserver to identify pockets on protein surfaces to predict binding sites for ligands
(
Original metaPocket webserver
)
LIGIN: Molecular docking using surface complementarity
TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations
MolSurfer: 2D Maps to Navigate 3D Structures of Proteins and their Complexes
ADS: Analytically Defined molecular Surfaces
PIPSA: Protein Interaction Property Similarity Analysis
SDA: Simulation of Diffusional Association
: Version 6
ECM: Effective (potential derived) Charges for Macromolecules in solvent
Our scripts for protein pKa calculations with the UHBD program
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