[Dock-fans] Carbohydrate docking in DOCK 6.2

Yunierkis Perez Castillo Yunierkis at uclv.edu.cu
Thu Jul 17 06:56:17 PDT 2008


I have found the same "strange" results with DOCK 6.2 when trying to dock small molecules, try 6.1, I get more realistic results with it than with 6.2
Yunierkis

________________________________________
From: dock-fans-bounces at docking.org [dock-fans-bounces at docking.org] On Behalf Of Mark J. Agostino [Mark.Agostino at vcp.monash.edu.au]
Sent: Wednesday, July 16, 2008 10:14 PM
To: dock-fans at docking.org
Subject: [Dock-fans] Carbohydrate docking in DOCK 6.2

Hello,

I have been trying to dock carbohydrates (2 to 4 saccharides in length) using DOCK 6.2 and am getting ridiculous results. I am seeing major steric clash between the saccharide rings. I have tried a multitude of things to fix the problem, including:

- Increasing number of minimisation steps (simplex_max_iterations, simplex_final_min_max_iterations and simplex_anchor_max_iterations)
- Turning on minimize_flexible_growth
- Changing anchor size (used 6 and 40)
- Selected more spheres for binding site (slightly expanded from cavity)
- Changed repulsive exponent in grid generation and docking run from 12 to 9 (repulsive_exponent in GRID input file and internal_energy_rep_exp in DOCK input file)
- Adjusted flex.defn to allow minimisation of some additional torsions (conj-oxygen and sp2-aromatic)
- Adjusted flex.defn to explicitly specify minimisation of glycosidic linkages (shown below)

          name         carb1
          drive_id      8
          minimize    1

          definition    C.3 ( H ) ( 2 O )
          definition    O ( C.3 ( H ) )

           name        carb2
           drive_id     8
           minimize   1

           definition   C.3 ( H ) ( 2 C. )
           definition   O ( C.3 ( H ) )

but none of this seems to generate good structures. The structures at the end look as if they have been crumpled up into a ball and placed in the binding site. I know that DOCK 4.0 used to work fine to dock carbohydrate structures, but now this seems somewhat broken in DOCK 6.2. Is there something I am overlooking here or is the problem something deeper in the program?

Thanks in advance,
Mark Agostino

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Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
-VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa María, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
-V Conferencia Científica Internacional de Ingeniería Mecánica, COMEC 2008, del 4 al 6 de noviembre de 2008, UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec

Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
-VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa María, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
-V Conferencia Científica Internacional de Ingeniería Mecánica, COMEC 2008, del 4 al 6 de noviembre de 2008,  UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec


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