Mobley Lab at UC Irvine (@MobleyLab)
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MobleyLab

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Top repositories

1

drug-computing

Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
Jupyter Notebook
142
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2

alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations
Python
111
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3

basic_simulation_training

A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be required for understanding/following many of the other "best practices" documents being prepared.
TeX
105
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4

FreeSolv

Experimental and calculated small molecule hydration free energies
Python
98
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5

benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
TeX
41
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6

Lomap

Alchemical mutation scoring map
Python
36
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7

Training

Lab policies, training, style guides, etc.
35
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8

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
Python
33
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9

SolvationToolkit

In-house tools for setting up arbitrary solute-solvent mixtures for simulation in GROMACS, Amber, OpenMM or other codes
Python
31
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10

GuthrieSolv

Experimental small molecule hydration free energy dataset
Python
30
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11

SeparatedTopologies

Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
Python
22
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12

chemper

Repository for Chemical Perception Sampling Tools
Python
19
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13

HiMap

High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
Python
16
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14

alchemical-setup

Python
15
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15

benchmarkff

Compare optimized geometries and energies from various force fields with respect to a QM reference.
Python
13
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16

DEL_analysis

Code to analyze the data from DNA-encoded libraries (DELs)
Jupyter Notebook
9
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17

off-ffcompare

Compare molecular structures after energy minimization in various force fields.
Jupyter Notebook
8
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18

D3R-2018-AutoDock-MMGBSA

binding affinity ranking using MM-GBSA and AutoDock score in D3R 2018
Shell
4
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19

mobleylab.org

Lab website
SCSS
4
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20

quanformer

quanformer: quantum mechanical analysis of molecular conformers
Python
3
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21

SMIRNOFF_paper_code

Code/tools relating to the initial SMIRNOFF format paper
Jupyter Notebook
3
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22

qm-theory-benchmark

Jupyter Notebook
3
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23

openff-spellbook

Handy functionality for working with OpenFF data
Python
3
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24

thermoML_data

Jupyter Notebook
2
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25

blues-water-hopping-paper

Contains files for blues-water-hopping paper
Python
2
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26

off_nitrogens

Exploring the planar or pyramidal nature of conjugated nitrogens
Python
2
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27

lysozyme_binding

Aggregator of binding data of small molecules to model binding sites in T4 lysozyme mutants, as popularized by Matthews, Shoichet and others.
Python
2
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28

wbointerpolation

Analysis scripts for the development of wiberg bond order interpolated parameters in the Open Force Field.
Jupyter Notebook
2
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29

orphans

Orphaned tools/scripts that might be useful but don't currently have a good home
Python
2
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30

slow-rotations

Python
2
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31

DEL_BB_design

Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies
Jupyter Notebook
2
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32

fitting-exp

Python
1
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33

gmx_fileprep

Scripts for local gromacs input file preparation
1
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34

gromacs-binding-scripts

Scripts relating to setup of binding studies for the GROMACS simulation package
1
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35

yank-restraints

Benchmarking project testing different restraints schemes for free energy calculations with Yank
1
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36

PME-RF-benchmark

Supporting information for a paper benchmarking PME vs RF performance for relative free energies
1
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37

waterNES

Workflows to calculate relative free energies using non-equilibrium switching for buried water molecules
Python
1
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38

Hydroxynator

Adjusts topology files with GAFF to have GAFF-DC charges
Python
1
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39

buried-water-electrostatics

We examined the electrostatic potential at the locations of buried waters within proteins to see if this exhibited any asymmetric behavior (previous work we had done suggested perhaps it might) and found none. Here's the code to reproduce.
Python
1
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