Re: CCL:question

[brian ^at^ bert.chem.wsu.edu (Brian W. Beck)]

 Dariusz C.Bienko wrote:
 :
 : Hi,
 : Have you ever heard about some theoretical calculation on
 : viruses? I think f.g. about some kind of geometry optimisations
 : of their full molecular shapes or any other simulations
 : related to viruses.
 :                                         Darek & Slawek
 :
 	Wade & McCammon did some work on HRV in 1992. I did a journal club
 	presentation on these articles. You might be able to use them
 	to boot-strap yourself to the latest stuff.
 	What follows is the references for the above articles:
 	(it's a two part article).
 Author:        Wade-R-C.  McCammon-J-A.
 Title:         Binding of an antiviral agent to a sensitive and a resistant
                human rhinovirus. Computer simulation studies with sampling of
                amino acid side-chain conformations. II. Calculation of
                free-energy differences by thermodynamic integration.
 Source:        J-Mol-Biol.  1992 Jun 5.  225(3).  P 697-712.
 Journal Title: JOURNAL-OF-MOLECULAR-BIOLOGY
 Subject Major: ANTIVIRAL-AGENTS: me.  OXAZOLES: me.  RHINOVIRUS: me.
                VIRAL-PROTEINS: me.
 Subject Minor: ANTIVIRAL-AGENTS: ch.  COMPUTER-SIMULATION.  CRYSTALLOGRAPHY.
                DRUG-RESISTANCE-MICROBIAL.  LEUCINE: ch.  MODELS-MOLECULAR.
                MOTION. OXAZOLES: ch.  RHINOVIRUS: ch.
                STRUCTURE-ACTIVITY-RELATIONSHIP. SUPPORT-NON-US-GOVT.
                SUPPORT-US-GOVT-NON-PHS.  THERMODYNAMICS. VALINE: ch.
                VIRAL-PROTEINS: ch.  WATER.
 Author:        Wade-R-C.  McCammon-J-A.
 Title:         Binding of an antiviral agent to a sensitive and a resistant
                human rhinovirus. Computer simulation studies with sampling of
                amino acid side-chain conformation. I. Mapping the rotamers of
                residue 188 of viral protein 1.
 Source:        J-Mol-Biol.  1992 Jun 5.  225(3).  P 679-96.
 Journal Title: JOURNAL-OF-MOLECULAR-BIOLOGY
 Subject Major: ANTIVIRAL-AGENTS: me.  OXAZOLES: me.  RHINOVIRUS: me.
                VIRAL-PROTEINS: me.
 Subject Minor: ANTIVIRAL-AGENTS: ch.  COMPUTER-SIMULATION.  CRYSTALLOGRAPHY.
                DRUG-RESISTANCE-MICROBIAL.  LEUCINE: ch.  MOLECULAR-STRUCTURE.
                MOTION.  OXAZOLES: ch.  PROTEIN-CONFORMATION.
                SUPPORT-NON-US-GOVT. SUPPORT-US-GOVT-NON-PHS.  THERMODYNAMICS.
                VALINE: ch. VIRAL-PROTEINS: ch.
 	-Brian
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