ADL: protein-protein docking

snoze pa at
Wed Oct 17 08:04:55 PDT 2007

yeah, it is possible but you have to deal with number of torsions in the
protein. Please refer following paper

*Science* 10 August 2001:
Vol. 293. no. 5532, pp. 1155 - 1159
DOI: 10.1126/science.1061692
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          Crystal Structure of a Neutralizing Human IgG Against HIV-1: A
Template for Vaccine Design

* Erica Ollmann Saphire,1 Paul W. H. I. Parren,2 Ralph Pantophlet,2 Michael
B. Zwick,2 Garrett M. Morris,1 Pauline M. Rudd,4 Raymond A. Dwek,4 Robyn L.
Stanfield,1 Dennis R. Burton,12* Ian A. Wilson13* *

We present the crystal structure at 2.7 angstrom resolution of the human
antibody IgG1 b12. Antibody b12 recognizes the CD4-binding site of human
immunodeficiency virus-1 (HIV-1) gp120 and is one of only two known
antibodies against gp120 capable of broad and potent neutralization of
primary HIV-1 isolates. A key feature of the antibody-combining site is the
protruding, finger-like long CDR H3 that can penetrate the recessed
CD4-binding site of gp120. A docking model of b12 and gp120 reveals severe
structural constraints that explain the extraordinary challenge in
eliciting effective
neutralizing antibodies similar to b12. The structure, together with
mutagenesis studies, provides a rationale for the extensive cross-reactivity
of b12 and a valuable framework for the design of HIV-1 vaccines capable of
eliciting b12-like activity.

On 10/10/07, Zheng Cai <zhengcai at> wrote:
> Hi everybody,
> I am trying to do a protein-protein docking using autoDock4. I wonder if
> you
> ever had any successful experience with the similar project? I would
> greatly
> appreciate if you could kindly share any info about that.
> Thanks~
> David
> --
> Zheng Cai, Ph.D.
> Department of Pathology and Laboratory Medicine
> University of Pennsylvania School of Medicine
> 252 John Morgan Building
> 36th Street and Hamilton Walk
> Philadelphia, PA 19104
> (lab-tel) 215-898-2870
> ________________________________________________
> --- ADL: AutoDock List  --- ---

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