User: se.raschka

gravatar for se.raschka
se.raschka140
Reputation:
140
Status:
Trusted
Location:
United States
Website:
http://sebastianraschk...
Twitter:
rasbt
Last seen:
4 years, 2 months ago
Joined:
5 years, 10 months ago
Email:
s*********@gmail.com

'Data scientist' and Machine learning enthusiast with a big passion for Python & open source. Author of 'Python Machine Learning'. Working on a novel molecular docking paradigm and a large-scale virtual screening library.

Posts by se.raschka

<prev • 14 results • page 1 of 2 • next >
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Answer: A: heatmap in R software or any software
... > Try heatmap.2 in the R gplots package. Yeah, that would be the "simplest" solution for basic heatmaps I'd say. I've put up a tutorials a few years ago, hopefully it helps regarding the details: [A short tutorial for decent heat maps in R][1] [1]: http://sebastianraschka.com/Articles/heatma ...
written 4.2 years ago by se.raschka140
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Tool: BioPandas - Working with molecular structures in pandas DataFrames
... Hi, all, I was working on a little library over the last few days and wanted to spread the news. It's a simple idea -- Working with molecular structures in pandas DataFrames -- but it comes in very handy in my computational biology work. It's of course open source, so please feel free to use it if ...
protein structure protein data bank pdb file tool written 4.5 years ago by se.raschka140 • updated 20 months ago by db410
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Tool: Energy minimization for hydrogen atoms only
... Hi, I am looking for a tool that optimizes the hydrogen-bond positioning in a protein-ligand complex without torsional or translational changes to the ligand or the protein residues.    Does anyone know about such a tool by chance?   It might sound a little bit weird, but I have an application ...
energy mininmization molecular docking tool written 5.4 years ago by se.raschka140
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Tool: PyProt - a Python package for working with protein structure files.
... PyProt is a Python package for working with protein structure files. It comes with a collection of ready-to-use scripts for the most common file operations and protein analyses. https://github.com/rasbt/pyprot Some time ago when I started with protein structure analysis, I wrote some simple functi ...
pdb protein tool mol2 written 5.5 years ago by se.raschka140
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Answer: A: How to use Autodock just for (re)scoring
... Okay, I finally figured it out in 6 simple steps.   1) Preparing a protein 2) Preparing a ligand 3) Generating a grid parameter file 4) Generating maps and grid data files 5) Generating a docking parameter file 6) Running AutoDock ...
written 5.9 years ago by se.raschka140
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Tutorial: Molecular docking, estimating free energies of binding, and a tutorial for how to use AutoDock's semi-empirical force field
... Discussions and questions about methods, approaches, and tools for estimating (relative) free binding energies of protein-ligand complexes are quite popular, and even the simplest tools can be quite tricky to use. Here, I want to briefly summarize the idea of molecular docking, and give a short over ...
tutorial docking scoring free energy written 5.9 years ago by se.raschka140
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Tool: A growing collection of "Free and useful protein-science tools"
... I thought that it might be useful to put together a list of the tools that I am currently using with a short description and usage example. I will add to it in future, and I am also looking forward to contributions: Please feel free to add your favorite tools if you like: https://github.com/rasbt/ ...
bioinformatics comutational biology tool written 5.9 years ago by se.raschka140
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Answer: A: MOL2 to PDBQT conversion via OpenBabel or MGLTools removes hydrogens
... Problem solved for AutoDock Vina:   The solution to the problem with `prepare_ligand4.py` would be prepare_ligand4.py -l my.mol2 -U \""" -C to keep the partial charges and hydrogen atoms (oddly, `-U ""` didn't work for me: `prepare_ligand4.py: option -U requires argument`) ...
written 5.9 years ago by se.raschka140
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MOL2 to PDBQT conversion via OpenBabel or MGLTools removes hydrogens
... I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms from the MOL2 file (the PDBQT file doesn't contain hydrogen atoms).   The command I used for OpenB ...
babel pdbqt mol2 written 5.9 years ago by se.raschka140
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Comment: C: A questionable practice: Dixon's Q test for outlier identification
... Especially in the case of n=3 with 1 "potential" outlier: Who is the outlier here? The 1 measurement or the other 2?  :) ...
written 5.9 years ago by se.raschka140

Latest awards to se.raschka

Autobiographer 4.5 years ago, has more than 80 characters in the information field of the user's profile.
Popular Question 5.4 years ago, created a question with more than 1,000 views. For MOL2 to PDBQT conversion via OpenBabel or MGLTools removes hydrogens
Popular Question 5.4 years ago, created a question with more than 1,000 views. For How to use Autodock just for (re)scoring
Scholar 5.9 years ago, created an answer that has been accepted. For A: MOL2 to PDBQT conversion via OpenBabel or MGLTools removes hydrogens
Scholar 5.9 years ago, created an answer that has been accepted. For A: MOL2 to PDBQT conversion via OpenBabel or MGLTools removes hydrogens

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