Thank you for your suggest, I will try right away.
> 在 2016年4月5日，上午9:50，David A Case <david.case.rutgers.edu> 写道：
>
> On Tue, Apr 05, 2016, YanhuaOuyang wrote:
>
>> In fact, I just have a fasta file of the protein sequence, I just don’t
>> know how to convert the peptide sequence to a pdb file of a protein
>> which is phosphorylated at Serine and Threonine. Can you tell me the
>> detailed steps.
>
> Converting a sequence to a (folded) structure is commonly called the "protein
> folding problem", and Google or Wikipedia can help you find lots of approaches
> to this. A *lot* depends on whether there is a known structure with a similar
> sequence (and how similar the sequences are). Amber is not generally the type
> of program one would use for homology modeling, nor for protein folding
> simulations, although the following paper shows some promising results:
>
> %A H. Nguyen
> %A J. Maier
> %A H. Huang
> %A V. Perrone
> %A C. Simmerling
> %T Folding Simulations for Proteins with Diverse Topologies Are Accessible in
> Days with a Physics-Based Force Field and Implicit Solvent
> %J J. Am. Chem. Soc.
> %V 136
> %P 13959-13962
> %D 2014
>
> If/when you get a three-dimensional structure that you have enough confidence
> in to continue, getting an initial structure with their phosphorylated
> analogues can be straightforward if the residues are surface exposed, as they
> are likely to be: remove the H atom connected to O on the side chain in the
> PDB file, rename the residues to their phosphorylated counterparts (you have
> to decide whether you want the mono-anion or di-anion forms), and let LEaP
> build in the phosphate groups. Then you have to hope that molecular dynamics
> can convert that rough starting structure into something that will be useful
> to you. Again, a *lot* depends on what you are trying to learn.
>
> This is a long-winded answer, but I hope it helps (both you and others
> interested in similar modeling exercises). You have to expect to spend time
> gaining experience, and understanding how simulation programs work. There are
> no "detailed steps" that will lead to success. The fact that you are
> asking how to convert a sequence to a PDB file suggests that you are new to
> our field; in that case, expect to spend a considerable amount of time and
> effort.
>
> ....regards...dac
>
>
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Received on Tue Apr 05 2016 - 05:00:03 PDT
