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Stars2
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LanguagePython
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License
GNU Lesser Genera... -
Created over 8 years ago
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Updated almost 3 years ago
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Repository Details
A pipeline for MSMs.
More Repositories
1
software-development
A primer on software development best practices for computational chemistry
254
2
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.Python
239
3
pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)Python
234
4
espaloma
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm πΉhttps://arxiv.org/abs/2010.01196Python
202
5
perses
Experiments with expanded ensembles to explore chemical spacePython
179
6
yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.Python
178
7
openmoltools
An open set of tools for automating tasks relating to small moleculesPython
63
8
ensembler
Automated omics-scale protein modeling and simulation setup.Python
52
9
openmm-tutorials
Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMMJupyter Notebook
48
10
mmtools
Some collected tools for molecular simulation pipelinesPython
41
11
qmlify
Jupyter Notebook
40
12
espaloma_charge
Standalone charge assignment from Espaloma framework.Python
34
13
ambermini
A stripped-down set of just antechamber, sqm, and tleap.C
30
14
gimlet
Graph Inference on MoLEcular TopologyPython
26
15
cpdetect
Change Point detectionPython
24
16
neutromeratio
Tautomer ratios in solutionJupyter Notebook
24
17
protons
OpenMM testbed for constant-pH methodologies.Python
21
18
thermopyl
Tools for ThermoML parsingPython
19
19
asapdiscovery
Toolkit for open antiviral drug discovery by the ASAP Discovery ConsortiumPython
19
20
torsionfit
Bayesian tools for fitting molecular mechanics torsion parameters to quantum chemical data.
Rich Text Format
19
21
assaytools
Modeling and Bayesian analysis of fluorescence and absorbance assays.Python
18
22
antibody-mutations
Assessing the impact of mutations on antibody-antigen binding affinityPython
17
23
pymbar-examples
Examples of applications of pymbar to various problems in simulation and experimentPython
16
24
automatic-equilibration-detection
Automatic detection of equilibrated regions of molecular simulationsTeX
16
25
pinot
Probabilistic Inference for NOvel TherapeuticsPython
15
26
chiron
Differentiable Markov Chain Monte CarloPython
14
27
feflow
Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkitsPython
13
28
integrator-benchmark
Code for enumerating and evaluating numerical methods for Langevin dynamics using near-equilibrium estimates of the KL-divergence. Accompanies https://doi.org/10.3390/e20050318Jupyter Notebook
12
29
yank-examples
Examples for use of YANK - getyank.orgPython
12
30
drug-gym
Reinforcement learning environments for drug discoveryJupyter Notebook
12
31
gibbs
Gibbs sampling for expanded ensembles and replica exchange simulationsPython
11
32
modelforge
Infrastructure to implement and train NNPsPython
11
33
perses-barnase-barstar-paper
Contains scripts and data for the perses barnase barstar paperJupyter Notebook
10
34
kinase-metadynamics
To run metadynamics simulations using openMM (based on Peter Eastman's script)Python
10
35
alchemy
Alchemical tools for OpenMMPython
9
36
cadd-grc-2013
Computer Aided Drug Discovery (CADD) GRC 2013 - slides, references, and examplesJupyter Notebook
9
37
yank-benchmark
Standard experimental accuracy benchmark set for YANK.Jupyter Notebook
8
38
nano-drugbank
Cheminformatic analysis of small molecule type drugs in DrugBank for their ability to form nanoparticles with indocyanine dyes.Jupyter Notebook
7
39
refit-espaloma
Refit espaloma with energies and forcesPython
6
40
sampl6-physicochemical-properties
SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)Jupyter Notebook
6
41
thresholds
Utilities for determining maximum tolerable timesteps. See https://doi.org/10.3390/e20050318Python
6
42
fah-xchem
Tools and infrastructure for automated compound discovery using Folding@homePython
6
43
charge-datasets
AM1-BCC ELF10 small molecule training datasetsPython
6
44
TargetExplorer
Database framework with RESTful API for aggregating genomic, structural, and functional data for target protein families.Python
6
45
saltswap
Package to fluctuate the number of counterions in an OpenMM simulationJupyter Notebook
6
46
autonomous-molecular-design
Sandbox for the development of active-learning algorithms for automated drug discovery.Jupyter Notebook
6
47
PDBfinder
a collection of scripts and files to help in PDB retrieval for various projectsPython
6
48
moldr
Manifold optimization for linear dimensionality reduction of MD trajectoriesPython
6
49
SETD8-materials
Code and data for SETD8 simulationsJupyter Notebook
5
50
wetlab-protocols
A collection of protocols, primarily for automated protein expression and mutagenesisPython
5
51
mtenn
Modular Training and Evaluation of Neural NetworksPython
5
52
bayesian-itc
Python tools for the analysis and modeling of isothermal titration calorimetry (ITC) experiments.TeX
5
53
rbd-ace2-contact-analysis
Code and workflow for running MD simulations on Folding@home to analyze RBD:ACE2 contactsPython
5
54
robots
Laboratory automation toolkitsPython
5
55
fah_prep
suite of functions to prepare simulations (docking, free energy) for use with folding at home.Python
5
56
ROCSALT
Dual topology alchemical free energiesPython
4
57
fahmunge
Tools for Munging Folding@Home datasetsPython
4
58
alchemical-playground
Tutorials, examples, and thoughts on alchemical free energy calculationsPython
4
59
openmm7tutorials
Tutorials using new features in OpenMM 7
AMPL
4
60
Ligandr
Ligandr codePython
4
61
fragmenter_data
Data for fragmenterJupyter Notebook
4
62
ring-open-fep
Ring-opening strategy for FEP.Python
3
63
clusterutils
Utilities for running parallel jobs with Torque/Moab and MPIPython
3
64
openmm-validation
[Work in progress] An extensive validation suite for the OpenMM molecular simulation library.Python
3
65
pdbbind_ml
Scripts to train and evaluate ML models on the PDBBind dataset.Python
3
66
nn-endstates
Jupyter Notebook
3
67
peptide-design
Design selective peptides targeting SH2 domainsJupyter Notebook
3
68
status
3
69
Ensembler2
Python
3
70
gbff
Tools for Bayesian forcefield developmentPython
3
71
resptools
Tools for multiconformer RESP fits using GAMESFortran
3
72
bellini
Bayesian Learning on Laboratory InvestigationPython
3
73
brokenyank
YANK: GPU-accelerated calculation of ligand binding affinitiesPython
3
74
docker-fah-client
Information on running the Folding@Home client inside a docker imagePython
3
75
pymbar-datasets
Python
3
76
SAMPL6-Reference-pKa-Calculations
Reference pKa calculations for the SAMPL6 pKa challengeJupyter Notebook
3
77
oeante
Antechamber (AMBER GAFF parameterization engine) implementation using OpenEye toolsPython
3
78
torsionfit_examples
examples and data for torsionfitJupyter Notebook
3
79
fluorescence_assay_working_data
Jupyter Notebook
3
80
itctools
Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.Python
3
81
mpiplus
Utilities to run on MPI.Python
3
82
msm-mfpt
Evaluating MSM-estimated mean first passage timesJupyter Notebook
3
83
DDR1_and_kinase_promiscuity_materials
Code and data for the paper 'What makes a kinase promiscuous for inhibitors?'.Jupyter Notebook
3
84
infiniteswitch
Implementation and testing of the infinite switch Hamiltonian exchange integrator.Python
3
85
MSMs
Markov state modelsJupyter Notebook
3
86
gcncharge
Graph convolutional networks for partial atomic chargesJupyter Notebook
3
87
kinalysis
Scripts for analyzing simulations of kinases!Python
2
88
papers-and-grants
YAML database of papers and grants from the Chodera labPython
2
89
harbor
A home for docking evaluation and assessmentPython
2
90
avoidome-analysis
A repository for downloading and analyzing the available Avoidome structuresJupyter Notebook
2
91
ERK-ancestral-materials
ERK ancestral reconstructionJupyter Notebook
2
92
duke-cbb-talk-2014-10-06
Slides from John Chodera's CBB talk at Duke University on 6 Oct 2014
2
93
assaytools2
Bayesian statistics-based assay modelling, accelerated by TensorFlow.Jupyter Notebook
2
94
enhanced-sampling-tmem175
Repository for running and assessing enhanced sampling simulations of TMEM175Jupyter Notebook
2
95
LDHA-MCCE
MCCE2 calculations for Lactate dehydrogenase A (collaboration with Thompson lab and Gunner lab)
Smarty
2
96
IR783-QSNAP
Analysis of Quantitative Structure-Nanoparticle Assembly Prediction (QSNAP) descriptors for predicting drug-indocyanine dye (IR783) nanoparticle formation.Jupyter Notebook
2
97
OpenMMEnergyComparisons
Comparisons of energies and forces between OpenMM and other packagesPython
2
98
hsa-affinity
All Human Serum Albumin affinity measurements will be deposited here.Jupyter Notebook
2
99
octomore
finding eight or more parameters we can try for applying openpathsampling to kinasesJupyter Notebook
2
100
kaizen
Continual improvement
2