rakeshr10 Goto Github PK

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

alphafold_non_docker

coe_workshop

Files related to the CoE workshop

deep-protein-structure-modeling

This repository is about prediction of tertiary structure of proteins from the primary structure of proteins (sequences of amino acids). So here, I'm trying to build a neural network that can input sequence of amino acids and output 3D structure of proteins (coordinates of major atoms in proteins that define the overall shape of the protein).

deeph3-distances-orientations

exospytosis

2019 - Open source project designed during the QBI/UCSF Hackathon with the objective of building a computationally efficient way of tagging vesicles events.

gromacsadaptivemd

Contains test trajectory for GROMACS based Adaptive MD

guacomole

guacomole recipes

hmrf-em-image

Hidden Markov Random Field Model and its Expectation-Maximization

hmrf-em-image_matlab

Implementation of the Hidden Markov Random Field Model and its Expectation-Maximization Algorithm

impopenmm

Experimenting with an interface to run OpenMM within IMP mainly to use OpenMM's MD engine

integrativestructuremodeling

Scripts, inputs and outputs used in the Integrative Structure Modeling of Spliceosomal Complexes

labmanual

Lab Manual for the Aly Lab at Columbia University

learn_cryoem_math

markov-random-field-project

This project has two parts. In part one, we use markov random field to denoise an image. In Part two, we use similar model for image segmentation.

markov-random-fields

Image denoising using Markov random fields.

meld-openmm-plugin

Meld plugin for OpenMM

mrf

A Python implementation of Markov Random Field (MRF) for image segmentation

mrf-segmentation-denoising

Probabilistic Graphical Models final project

mrf2d

An R package for analysis of Markov Random Fields on 2-dimensional lattices.

mrfdenoise

Markov Random Field

multislice

Scripts for calculating simulated transmission electron microscopy images based upon PDB files

nbspike

Integrative modeling of nanobody binding modes to the SARS-CoV-2 Spike protein

openmm-cookbook

A collection of code snippets for doing molecular simulations with OpenMM.

peptidebuilder

presentations

Presentations folder for all my files

python-machine-learning-fundamentals

D-Lab's 6 hour introduction to machine learning in Python. Learn how to perform classification, regression, clustering, and do model selection using scikit-learn and TPOT.

pytorchexp

Experimenting with Pytorch for deeplearning

rakeshr10

Config files for my GitHub profile.

rsa-normalization-values