Thanks Great!
See these tools very useful
Server (URL) Function Required input
http://ftmap.bu.edu <
http://ftmap.bu.edu/> Identifying binding hot spots; determining druggability; providing information for fragment-based drug discovery PDB ID of a protein, DNA or RNA structure, or structure file in PDB format
http://ftsite.bu.edu <
http://ftsite.bu.edu/> Identifying likely ligand-binding sites; ranking of sites in terms of probe-protein interactions; listing of binding site residues PDB ID of a protein structure, protein structure file in PDB format, or a zip file containing up to 15 protein PDB files
http://ftflex.bu.edu <
http://ftflex.bu.edu/> Identifying binding hot spots of proteins and determining druggability, while accounting for side-chain flexibility around selected hot spots; opening pockets in protein-protein interfaces Stage 1: PDB ID of a protein structure, or protein structure file in PDB format
Stage 2: selection of hot spots for side-chain adjustment and remapping
http://ftmap.bu.edu/param/ <
http://ftmap.bu.edu/param/> Same as FTMap, plus determining the low-energy binding poses of up to 15 user-selected probe molecules in hot spot regions PDB ID of a protein, DNA or RNA structure, or a structure file in PDB format; plus formal charges and SMILES strings to define additional probes
http://ftdyn.bu.edu <
http://ftdyn.bu.edu/> Mapping potentially large ensembles of protein structures; determining probe-protein interactions for each structure, and averages over the ensemble; identifying the structure most similar to a ligand-bound conformation Ensemble of protein structures specified in PDB model record format
Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 31 Mar 2016, at 5:10 PM, Ofir Tal <pantufel.hotmail.com> wrote:
>
> Dear Michael,
>
> Recently I found this paper, might be useful.
>
> Good luck,
> Ofir.
>
> Methods Mol Biol. 2015 ; 1215: 253–287. doi:10.1007/978-1-4939-1465-4_12.
> Accelerated Molecular Dynamics and Protein Conformational
> Change: A Theoretical and Practical Guide Using a Membrane
> Embedded Model Neurotransmitter Transporter
> Patrick C. Gedeon, James R. Thomas, and Jeffry D. Madura
>
>
>
> Dr. Ofir Tal, PhD
> Structural Bioinformatics
> Bioinformatics Knowledge Unit - BKU
>
> http://bku.technion.ac.il/
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of TechnologyHaifa 32000, ISRAEL
> pantufel.technion.ac.il
>
>
>> From: michael.shokhen.biu.ac.il
>> To: AMBER.ambermd.org
>> Date: Thu, 31 Mar 2016 10:07:56 +0000
>> Subject: Re: [AMBER] aMD simulation of membrane protein ?
>>
>> Both - protein and membrane must be accounted as solute
>> in aMD parameters settings.
>>
>> Michael
>>
>>
>>
>>
>>
>> ________________________________________
>> From: Michael Shokhen <michael.shokhen.biu.ac.il>
>> Sent: Wednesday, March 30, 2016 1:18 PM
>> To: AMBER.ambermd.org
>> Subject: [AMBER] aMD simulation of membrane protein ?
>>
>> Dear Amber experts,
>>
>> I have Amber14 and AmberTools15, and I want to apply aMD
>> accelerated MD for the simulation of membrane protein.
>>
>> The AMBER "Advanced Tutorial 22 Introduction" describes
>> an example of water solvated protein aMD simulation,
>> so I have some questions about the aMD protocol application
>> for membrane proteins.
>>
>> 1.
>> The parameter setting in the tutorial defines E(dih) and Alpha(dih)
>> for solute atoms only that is protein in the tutorial:
>>
>>
>> c) EthreshD: E(dih)=595 kcal mol-1 + (4kcal mol-1 residue-1 * 58 solute residues) = 827 kcal mol-1
>>
>> d) alphaD: Alpha(dih)=(1/5)*(4kcal mol-1 residues-1 * 58 solute residues) = 46.4 kcal mol-1
>>
>> Do I need to extend the E(dih) and Alpha(dih) setting on membrane lipid molecules also?
>>
>>
>> 2. I would appreciate if somebody address me to any published
>> amber protocol of membrane protein aMD simulation.
>>
>> Thank you,
>> Michael
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 31 2016 - 08:30:03 PDT
