Repositories list

• PDBBind-Opt

  Public
  Workflow to clean up and fix structural problems in protein-ligand binding datasets

  Jupyter Notebook

  •1•9•0•0•Updated Nov 5, 2024Nov 5, 2024

• CSpred

  Public
  UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted from the 3D structures of the proteins.

  Jupyter Notebook

  •6•17•3•3•Updated Oct 3, 2024Oct 3, 2024

• H2Combustion_BO-POL

  Public
  Wiberg/Mayer Bond Indices and Polarizabilities for the Hydrogen Combustion Dataset IRC's

  Jupyter Notebook

  •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

• NewtonNet

  Public
  A Newtonian message passing network for deep learning of interatomic potentials and forces

  Python

  •

  MIT License

  •12•32•3•1•Updated Jul 30, 2024Jul 30, 2024

• MLHessian-TSopt

  Public
  Jupyter Notebook

  •

  MIT License

  •1•8•1•0•Updated Jul 29, 2024Jul 29, 2024

• ptm_sc

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Apr 22, 2024Apr 22, 2024

• iShiftML

  Public
  Predicting CCSD(T)/CBS level chemical shieldings for H/C/N/O using wB97X-V/pcSseg-1 level DFT calculations

  Python

  •

  MIT License

  •1•3•0•0•Updated Apr 17, 2024Apr 17, 2024

• LP-PDBBind

  Public
  Jupyter Notebook

  •3•30•1•0•Updated Jan 29, 2024Jan 29, 2024

• PiContact

  Public
  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 15, 2023Oct 15, 2023

• H2Combustion_AL

  Public
  Python

  •

  MIT License

  •0•2•2•0•Updated Sep 25, 2023Sep 25, 2023

• Pseudopotential

  Public
  0•2•0•0•Updated Aug 23, 2023Aug 23, 2023

• X-EISDv2

  Public
  Generalized, modular, and faster version of X-EISD: Extended Experimental Inferential Structure Determination

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Aug 3, 2023Aug 3, 2023

• MCSCE

  Public
  Monte Carlo Side Chain Entropy package for generating side chain packing for fixed protein backbone

  Python

  •

  MIT License

  •2•3•2•1•Updated Jul 25, 2023Jul 25, 2023

• DynamICE

  Public
  A generative-reinforcement model (RL-GRNN) to generate new IDP conformer ensembles biased towards experimental data.

  Python

  •

  MIT License

  •0•1•0•0•Updated May 3, 2023May 3, 2023

• int2cart

  Public
  Building more accurate protein structures from backbone torsion angles

  Python

  •5•14•1•0•Updated Feb 8, 2023Feb 8, 2023

• mbucb-tinker

  Public
  Fortran

  •0•0•0•0•Updated Jul 10, 2022Jul 10, 2022

• sidechainnet

  Public
  An all-atom protein structure dataset for machine learning.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •38•0•0•0•Updated May 11, 2022May 11, 2022

• M-X--H2O-6-8

  Public
  0•0•0•0•Updated Nov 2, 2021Nov 2, 2021

• cubedipole

  Public
  A code to calculate the bond dipole moment.

  0•0•0•0•Updated Sep 17, 2021Sep 17, 2021

• H2COMBUSTION_DATA

  Public
  DFT data for the hydrogen combustion reaction obtained at the level of wB97X-V/cc-pVTZ level. The data consists of energies and atomic force vectors of all 19 reaction channels involved in the combustion reaction. For reaction channel 6 two spin state calculations performed triplet and singlet states, named as 06a and 06b. Similarly, reaction ch…

  Python

  •0•2•1•0•Updated Sep 7, 2021Sep 7, 2021

• Useful_scripts

  Public
  Python

  •0•2•0•0•Updated Sep 6, 2021Sep 6, 2021

• X-EISD

  Public
  X-EISD – Extended Experimental Inferential Structure Determination

  Python

  •

  MIT License

  •2•2•0•0•Updated Apr 17, 2021Apr 17, 2021

• 3D-DenseNet-ChemShift

  Public
  Python

  •2•3•0•0•Updated Apr 5, 2020Apr 5, 2020

• cool-walking

  Public
  Python

  •0•1•0•0•Updated Nov 19, 2019Nov 19, 2019