Questions tagged [computational-biochemistry]
The computational-biochemistry tag has no usage guidance.
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How to create an Alchem configuration file for NamD simulation?
I am trying to use NamD for Alchem simulation for a bilayer system. I am using the script below as the configuration file, but after the minimization step, I am getting this error: "FATAL ERROR: ...
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Creating hybrid topology using VMD
I wanna create a Hybrid topology for alchemical free energy calculation.
I am using the VMD plugin mutator to create that hybrid topology. But, I am facing this Error: unable to load structure file ...
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Parsing pre-2007 SMILES string
How would one parse the SMILES string
BrC[2]:C[3]:C(:CH:CH:CH:@2):CH:CH:CH:CH:@3
I rely on tools like rdkit and ...
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What is the difference between flat and stereo stitch id?
For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (http://sideeffects.embl.de/download/). If you open the README file, ...
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How to generate chemical picture from SMILES code with OPEN Babel?
I would like to generate a chemical picture of some nucleosides from their SMILES code. I found this fancy generator on the internet. The layout is of course based on OpenBabel.
I would like to know ...
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Converting miRNA names to miRBase version IDs
I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example:
hsa-miR-106a ---> hsa-miR-106a-5p
hsa-miR-373* --> hsa-miR-373-5p
hsa-miR-33 --> hsa-miR-33a-5p
...
- 11
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186
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How to convert amino acid sequence to SMILES format
I have an amino acids string "MKGK" and I would like to convert it into SMILES format.
I tried two approaches.
First with PepSMI which gives me:
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general cheminformatics references
Can anyone explain what is cheminformatics and how does it help in the future?
I need to write an article that should be understandable for 14-20 yr age group. Please help with references, I don't ...
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How to download the whole genome of an organism from NCBI using R or Python?
I need to download some of the genomes of human gut microbiome in FASTA format. Anybody has any script to download?
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Do you know any virtual screening libraries with small, soluble compounds?
I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
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Building small molecules de novo
Can anyone recommend a protocol for building the 3D structure of a small molecule de novo, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, ...
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Are codons in RNA layered? Are we misinterpreting RNA codons?
I am analyzing nucleotide base-pair patterns in RNA and DNA, and had a thought about RNA and DNA (Let me first state though, I am not a biologist; I am an algorithmatician, employing a sort of ...
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How are different forcefields developed/evaluated?
The Rosetta software can use a variety of different energy functions:
Ref2015
GenPot
Beta-Nov16
How are these energy functions developed and validated? Is it common to do a single protein design ...
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68
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B-factor analysis in nanobodies
I am doing my research on nanobodies. Currently, I am trying to do a comparison study of the flexibility of CDR loops using B-factor values. I would like to know if there is any statistical analysis ...
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Issues with AutoDock Vina
I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
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Question about Using MDAPackmol (packmol in python)
I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on GitHub so I can gain an ...
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How do I convert an Excel file (.xlsx) to an .smi file format?
How do I convert an Excel file(.xlsx) to .smi file format?
The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
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How many models should be generated by rosetta for denovo protein structure prediction?
How many models should be generated by rosetta for de novo protein structure prediction of a 382 long sequence? In the tutorial, it says 50,000 models but practically it takes a lot of time (weeks) to ...
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