14 Works

A Benchmark Data Set for Hydrogen Combustion

Akshaya Das, Christopher J. Stein, Farnaz Heidar-Zadeh, Luke Bertels, Meili Liu, Xingyi Guan, Mojtaba Haghighatlari, Jie Li, Oufan Zhang, Hongxia Hao, Itai Leven, Martin Head-Gordon & Teresa Head-Gordon

gREST_SSCR simulation of trimeric SARS-CoV-2 Spike protein starting from 1Up conformation

Hisham Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung & Yuji Sugita

Python Data and Scripting Workshop for Computational Molecular Scientists

Ashley Ringer McDonald & Jessica Nash

3k bound SARS-CoV PLPro

Chia-en Chang, Yuliana Bosken & Timothy Cholko
1μs MD trajectory generated using Amber, FF14SB force field trajectory, GAFF2 for ligand, AM1-BCC charges for ligand; stripped of water molecules and counter ions.

Apo SARS-CoV-2 PLPro (from PDB 6WRH C-chain)

Chia-en Chang, Yuliana Bosken & Timothy Cholko
1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.

Multiscale models for the SARS-CoV-2 Virion

Yu Alvin & Gregory Voth
This repository contains coarse-grained (CG) models for the SARS-CoV-2 virion developed under an NSF RAPID award 2029092 to G.A.V. in response to the COVID-19 pandemic.

ANI-FDA Drugs Archive

Olexandr Isayev
The dataset files contain low-energy conformers and tautomers of 6,433 FDA approved & investigational drugs. A collection consists of 32,036 tautomeric structures and ~3M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). [DOI: 10.26434/chemrxiv.11819268.v1 ] For each conformer we list total energy, relative energy, and dipole-consistent partial atomic charges....

ANI-CAS Antiviral Archive

Olexandr Isayev
The dataset files contain low-energy conformers and tautomers for 20,306 from the CAS Antiviral database. Original ~50K molecules were filtered for duplicates and drug-likeness. A collection consists of 67,167 tautomeric structures and ~6.6M conformers. After extensive sampling, for every tautomer we found low laying conformers within approx. 6 kcal/mol window using ANI-2x neural-network molecular potential. [DOI: 10.26434/chemrxiv.11819268.v1 ] The ANI-2x potential is approaching the accuracy of high-level QM calculations (wB97x-D). For each conformer we list...

SARS-COV-2 Coarse Grained Viron Model

Alvin Yu & Gregory Voth
A coarse-grained (CG) model for the SARS-CoV-2 virion developed under an NSF RAPID award 2029092 to Gregory A Voth in response to the COVID-19 pandemic.

Apo SARS-CoV PLPro

Chia-en Chang, Yuliana Bosken & Timothy Cholko
1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.

Apo SARS-CoV-2 PLPro (from PDB 6W9C C-chain)

Chia-en Chang, Yuliana Bosken & Timothy Cholko
1μs MD trajectory generated using Amber, FF14SB force field trajectory, stripped of water molecules and counter ions.

3k bound SARS-CoV-2 PLPro (3k docked to frame from trajectory of PDB 6W9C C-chain)

Chia-en Chang, Yuliana Bosken & Timothy Cholko
1μs MD trajectory generated using Amber, FF14SB force field trajectory, GAFF2 for ligand, AM1-BCC charges for ligand; stripped of water molecules and counter ions.

Best Practices in Python Package Development

Jessica Nash, Doaa Altarawy, Taylor Barnes, Samuel Ellis, Eliseo Marin Rimoldi, Benjamin Pritchard & Daniel Smith

gREST_SSCR simulation of trimeric SARS-CoV-2 Spike protein starting from Down conformation

Hisham Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung & Yuji Sugita

Registration Year

  • 2021
    5
  • 2020
    9

Resource Types

  • Model
    7
  • Dataset
    5
  • Other
    2

Affiliations

  • University of California, Riverside
    5
  • University of Chicago
    2
  • Molecular Sciences Software Institute
    2
  • Carnegie Mellon University
    2
  • California Polytechnic State University
    1
  • University of California, Berkeley
    1
  • Beijing Normal University
    1
  • Lawrence Berkeley National Laboratory
    1
  • Queen's University
    1
  • University of Duisburg-Essen
    1