zagrosman

I am an academic freelance researcher, working on natural products, protein-protein interactions, plant-microbiome interactions and playing with R codes :)

Iran

Pinned Repositories

biocode
Bioinformatics code libraries and scripts
Language:Python10
BioR
Herein, I'll try to develop R scripts for Biotechnologists who want to expand their idea easily.
Language:R1 1 00
chemminetools
ChemMine Tools: open source web framework for small molecule analysis
Language:JavaScript1 0 00
FastScript
This page will provide highly fast-running python scripts for biologists and biotechnologists. I want to develop my ideas to help my colleagues all over the world for saving their time during computational analyses.
Language:Jupyter Notebook6 2 03
fpocket-cavity-finder
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).
Language:C1 0 00
MPBuilder
MPBuilder provides building capability for protein-detergent, bicelle, and lipid-scaffold (saposin nanoparticles, nanodiscs) complexes and links this to the ATSAS software package modules for model refinement and validation against the SAXS data.
Language:Python1 0 00
pteros
Modern and fast molecular analysis and modeling library for C++ and Python
Language:C++1 0 00
pymod
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Language:Python1 0 00
RNArtist
RNArtist allows you to design and paint your RNA 2D structures interactively. Coupled with the 3D viewer UCSF Chimera, use your 2D as a map to explore RNA 3D architectures.
Language:Kotlin10
Students
Free tools for biologists and biochemists
Language:Python61

zagrosman's Repositories

zagrosman/2019-06-04-NMNH
Repository for the Genome Annotation Workshop at NMNH (June 4-5, 2019)
zagrosman/adobe-illustrator-for-beginners
Source files for Tuts+ course: Adobe Illustrator for Beginners
zagrosman/BioinforMatikz
BioinforMatikz tools
zagrosman/BondPack
A collection of PyMOL plugins to visualize atomic bonds.
zagrosman/CavBench-cavitiy-finder
CavBench is a generic and extensible benchmark to compare different protein cavity detection methods relative to diverse ground truth datasets.
zagrosman/CCTopStandalone
zagrosman/Christmas_tree_protein
A Christmas tree protein
zagrosman/circos
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.
zagrosman/cluspro-tools
Provides tools for analyzing ClusPro protein docking results
zagrosman/Cluspro_crawler
Language:Python0 0
zagrosman/deepPromoter
Classifying promoters using deep learning and fastText features
Language:Python0 0
zagrosman/deltaVinaXGB
This is a machine-learning based protein-ligand scoring function.
zagrosman/EasyDockVina2
EasyDockVina: Graphical User Interface for Ligand Optimization and Molecular Docking with AutoDock Vina.
zagrosman/EDNAtran
Language:Shell0 0
zagrosman/Enhanced_Sampling_Methods_Tutorials
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
Language:Shell0 0
zagrosman/find_circ
tools to find circRNAs in RNA-seq data
zagrosman/gmx_tutorials_livecoms
LiveCoMS GROMACS Tutorials Paper
zagrosman/GoodSell-Illustrate
Biomolecular Illustration Tool
Language:Fortran0 0
zagrosman/IRscope
zagrosman/litsearchr-tutorial
A tutorial for the R package 'litsearchr'
zagrosman/mpi-vina
An MPI based parallel implementation of Autodock Vina
zagrosman/pmw-patched
Fork of Python megawidgets with essential patches applied
zagrosman/Protein-refinement-
zagrosman/protein_fuser
A py3 script to fuse structures together
zagrosman/pytoefl
Simulate toefl independent speaking test on python script
zagrosman/Restaurant-Picker
This project includes a simple example of a restaurant picker, which was introduced in my "Introduction to Python with Anaconda for Beginners".
zagrosman/shinyCircos
an R/shiny application for creation of Circos plot interactively
zagrosman/SRA-tutorials
In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given that you give proper credit. Have fun!
zagrosman/Tutorial1-Normalization-Rnaseq
RNA-seq, R tutorial
zagrosman/Virtual-Screening-files