LINB PROJECT

• Biedermannova_August_September_2009_LinB_ramd.pdf First insights into the ligand exit pathways in LinBwt and LinBL177W using RAMD simulations. [28-September-2009]

• Biedermannova_July_2009_ramd_params.pdf Initial RAMD simulations of LinBwt and LinBL177W. [19-August-2009]

• Biedermannova_June_2009_LinB.pdf Computational study of product release in LinB haloalkane dehalogenase. [15-July-2009]

DHLA.DCE PROJECT

• Application of Locally Enhanced Sampling for Study of 1,2-Dichloroethane Binding to the Haloalkane Dehalogenase DhlA

• Application of Molecular Dynamics for Study of Substrate Binding and Reaction Mechanism of Haloalkane Dehalogenase DhlA

DHAA.TCP PROJECT

• Parametrisation of (S)-2,3-dichloro-1-propanol (S-DCL) for AMBER Force Field

• Molecular Docking of 1,2,3-trichloropropane (TCP) to Free DhaA and (S)-2,3-dichloro-1-propanol (S-DCL) to DhaA.Cl- Complex by AUTODOCK

• Parametrisation of (R)-2,3-dichloro-1-propanol (R-DCL) for AMBER Force Field

• Molecular Docking of (R)-2,3-dichloro-1-propanol (R-DCL) to DhaA.Cl- Complex by AUTODOCK

• Planned Random Expulsion Molecular Dynamics (REMD) Simulations

• Equilibration Molecular Dynamics on DhaA with Products of 1,2,3-Trichloropropane Dehalogenation

pH OPTODE

• Monitoring of Haloalkane Dehalogenase Reaction by Using pH Optode: Screening of Specificity and Evaluation of Kinetic Constants

NATO PROJECT MEETING - BRNO

• Dehalogenase-Based Optical Biosensors for Contaminant Monitoring

• Pictures

PROJECT REPORT TO NATO - 2005

• 2005 report to NATO- scientific part

NATO PROJECT MEETING - HANNOVER 2006

From Brno:

• Jiri: projects overview (pdf)

• Jiri: On phylogeny (pdf)

• Jiri: On ramd (pdf)

• Zbynek: on TCI and enantioselectivity (pdf)

From Heidelberg:
The techniques that Rebecca talked about are available at these links:

• ProSAT2

• RAMD in AMBER8

From Madrid:

• Ana and Federico: Results (xls)