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31 views

PQR files make from pdb2pqr are different to GROMACS

I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce pqr, with topol.top taken from pdb2gmx and use it to produce pdb file, then use pdb2pqr. Which one is ...
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1answer
72 views

What are the areas a student must focus before entering the computational biology research?

I am not a biologist. But highly motivated by the recent advancements and problems in modern biology. I have been shortlisted for a PhD(computational biology programme at IMSc, Madras) interview in ...
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35 views

How to simulate a carbon nanotube in water using NAMD and VMD?

I am learning how to use NAMD and VMD to simulate carbon nanotubes. The NAMD tuturial does not provide examples of equilbrating nanotubes. Could someone one provide an example of nanotube in water? ...
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1answer
51 views

“boundary” vs “interface”?

I am working with biofilm and there are many documents talking about boudary conditions while others talks about interface or both of boundary and interface. So, boundary and interface are the same ...
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0answers
29 views

Statistical Coupling Analysis (SCA) to identify coevolved residues in protein families: use of ICA

This is a computational (structural) biology question. We've recently begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the ...
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1answer
101 views

Calculating AIC (in R or any other statistical software)

I am trying to fit the log-log plot of the cumulative distribution of a network to one of three models: Exponential (EXP) ($P(k)\sim e^{-ak}$), Exponentially truncated power law (TRU) ($P(k)\sim ...
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4answers
992 views

Are open-source codes available to study protein folding?

I would like to test the influence of solvation parameters in implicit solvation models and wonder which codes are freely available as standalone programs for protein folding of small proteins, and ...
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0answers
49 views

Assembled human ESTs for annotation

I am annotating protein-coding genes in a region of the human genome and am looking for a set of assembled ESTs I can use as evidence for constructing gene models. A quick search of NCBI's SRA shows ...
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1answer
144 views

Global optimal sequence alignment algorithms

As far as global optimal sequence alignment goes, is the Needleman-Wunsch and Hirschberg's algorithm still state of the art? Or have there been any improvements to these algorithms since they were ...
3
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1answer
142 views

Artificial RNA 3D folding

I have a 50-base, artificially created RNA sequence and I would like to obtain its 3D structure. What software should I use for this purpose?
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984 views

Parsing protein structure data in C

My background is in genomics, but I have recently been working with problems related to protein structure. I wrote a few relevant programs in C, building my own PDB file parser from scratch in the ...