gundalav

How reliable is Alphafold2 for folding random-coil peptide

2

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography,...

Openmm Example for Protein-Ligand Complex

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Hi, Thanks for making this great tool. Is there anywhere I can find example or tutorial for Protein-Ligand Complex modeling? I'm thinking of something like [GROMACS tutorial of the same...

Fine tuning which variable to smooth in GAM

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As far as I understand, currently we have to manually which variable to smooth. In the [example](https://community.rstudio.com/t/tune-grid-and-gam-model-incl-gam-formula/127206) below: ``` library(tidymodels) #> Registered S3 method overwritten by 'tune': #> method from...

Indexdb died error message when creating colabfold_envdb_202108_db with MMseqs

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Hi, I was trying to setup the database. But it breaks upon the execution of this code: `mmseqs createindex colabfold_envdb_202108_db tmp2 --remove-tmp-files 1 ` The error message I get is...

How to calculate the binding energy from multimer complexes made by Alphafold2

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I have a structure created with Multimer option. The complex is created by giving the ligand and receptor amino acid sequences. I presume it is conceptually the same as 'docking'....

Hi, Thank you for making this great package. First of all this is not about issue in the code. But a usage question. AFAIK the key parameters in Peptide builder...

Hichipper on DNase/Mnase type of data (no Resfrag required)

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Hi Caleb, Is there a way to run HICHIPPER on the data that doesn't require ResFRAG? The data such as DNAse/MNase. I know that HiC-Pro provide such [possibility](http://nservant.github.io/HiC-Pro/USER_CASES.html). Thanks and...