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Questions tagged [computational-biochemistry]

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Best reference book for basic concepts when working with bioinformatics

I'm starting to study Bioinformatics, I already have basic knowledge of Biochemistry and Genetics, but I want to buy a reference book, to use when I forget a concept (I'm a Computer Science student, ...
1 vote
1 answer
34 views

Seeking Guidance on Designing DNA Sequences with Specific Criteria

Dear Bioinformatics Community, I hope you're all doing well. I am currently working on a project that requires designing some 10 nucleotide single-stranded DNAs, (preferably), with specific criteria. ...
2 votes
0 answers
9 views

SHAP correlation patterns for model prediction of protein are confusing

I have developed an ANN model to predict protein post-translational modification patterns from Elisa data. For simplicities sake, the how, feasibility and parameters aren't important for my question ...
2 votes
0 answers
240 views

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, ...
0 votes
0 answers
18 views

Seeking Advice on Acquiring Clean Experimental data comprises of proteins for FDR Estimation

I am a bioinformatics student doing my research on top-down mass spectrometry-based proteomics and seeking some guidance on acquiring very clean experimental data with known true positives and false ...
1 vote
2 answers
84 views

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 ...
1 vote
0 answers
19 views

Which components must be included in the HDR plasmid?

I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues. I wanted to know exactly which components must be included in the plasmid. I know that I have ...
3 votes
1 answer
63 views

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 ...
1 vote
0 answers
87 views

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 ...
1 vote
1 answer
2k views

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: ...
-1 votes
1 answer
45 views

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 ...
2 votes
1 answer
231 views

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?
0 votes
1 answer
41 views

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, ...
2 votes
2 answers
121 views

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 ...
1 vote
2 answers
178 views

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 ...
0 votes
1 answer
123 views

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 ...
0 votes
0 answers
212 views

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.
1 vote
0 answers
136 views

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 ...
3 votes
1 answer
106 views

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 ...
0 votes
1 answer
389 views

How to specify input resfile for Rosetta?

I'm trying to run the following Rosetta command. ...
0 votes
1 answer
590 views

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 ...