Jensen Group (@jensengroup)
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Top repositories

1

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
Python
234
star
2

xyz2mol

Converts an xyz file to an RDKit mol object
Python
204
star
3

molcalc

MolCalc is a web interface that allows anyone to build molecules and calculate molecular properties online
HTML
73
star
4

GB_GA

Graph-based genetic algorithm
Python
68
star
5

GB-GM

Graph-based generative model
Python
19
star
6

protonator

Quick and dirty protonation
Jupyter Notebook
15
star
7

fragbuilder

fragbuilder is a tool to create, setup and analyze QM calculations on peptides.
Python
14
star
8

atom_mapper

Atom order in one molecule is made to match that in another
Python
10
star
9

RegioSQM

See http://dx.doi.org/10.1039/C7SC04156J for more details
Python
9
star
10

compute_pka

Computes apparent pKa values from QM dat
Python
8
star
11

FP_RF_XAI

Jupyter Notebook
8
star
12

molstat

Molecular Statistics
TeX
8
star
13

take_elementary_step

Python
8
star
14

propka-3.0

PROPKA predicts the pKa values of ionizable groups in proteins based in the 3D structure.
Python
7
star
15

mol_gen

Molecule generation and optimization
Python
7
star
16

GA_ChemSpace_exploration

Jupyter Notebook
6
star
17

mbh_catalyst_ga

Catalyst design for the Morita−Baylis−Hillman Reaction using a graph-based genetic algorithm
Python
6
star
18

get_conformations

generate molecular conformations
Python
6
star
19

String-GA

String-based genetic algorithm
Python
5
star
20

RegioML

RegioML predicts the regioselectivity of electrophilic aromatic substitution reactions using machine learning.
Python
5
star
21

AutomatedReactionsMetaMD

Python
4
star
22

RegioSQM20

RegioSQM20 predicts the regioselectivity of electrophilic aromatic substitution reactions in heteroaromatic systems.
Python
4
star
23

ReactionDiscovery

Python
4
star
24

dha_htvs

Jupyter Notebook
4
star
25

molget

Generates molecular coordinates from chemical name using Babel and Cactus
Shell
4
star
26

HeckQM

A QM-based workflow for determining the regioselectivity of palladium-catalyzed Heck reactions.
Jupyter Notebook
4
star
27

procs

A Protein Chemical Shift Predictor
Python
3
star
28

smiles2coord

bash script to get coordinates from SMILES and Cactus.
Shell
3
star
29

TS_conf_search

Conformer search for transition states
Python
3
star
30

molcalc-1.3

MolCalc version 1.3 (php)
JavaScript
3
star
31

fragreact

Molecular reaction fragmentation scheme towards improving the accuracy of enthalpy calculation
Python
3
star
32

db-enzymes

Database of reaction barriers in proteins with structures
Python
3
star
33

statsig

Determination of statistical significance using composite errors
Python
3
star
34

MBH_CatalystDiscovery

Jupyter Notebook
2
star
35

procs15

DFT-based chemical shift predictor
C++
2
star
36

SI_RegioSQM20

Jupyter Notebook
2
star
37

CHSQM

Prediction of labile carbon hydrogens using semiempirical methods
Python
2
star
38

protonate

Python
2
star
39

RMSD_PP_TS

Locate TS based on RMSD-PP method
Python
2
star
40

optimized-protein-structures

Collection of optimized protein structures
2
star
41

xtb_gaussian

Python
1
star
42

find_heteroaromatic_rings

Python/RDKit script that finds unique heteroaromatic rings in a list of SMILES strings
Python
1
star
43

GED

Computes the graph edit distance between 2 graphs using RDKit and Networkx
Python
1
star
44

rdkit_qm_utilities

Python
1
star
45

db-regioselectivity

A database of compounds and their regioselective products
TeX
1
star
46

prohxms

Simple Protein HXMS prediction frame work with BioPython.
Python
1
star
47

procs-phaistos

ProCS amide proton chemical shift predictor module for Phaistos
C++
1
star
48

xyz2sdf

Python
1
star
49

camshift-phaistos

PHAISTOS module containing an implementation of the CamShift chemical shift predictor
C++
1
star
50

hydrogen-bond-correction-f3

Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields
Fortran
1
star
51

GA_schrock

Genetic algorithm for evolution of the Schrock catalyst.
Python
1
star