Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: ParmEd

https://packages.ecosyste.ms/registries/pypi.org/packages/ParmEd

Inter-package toolkit for molecular mechanical simulations
16 versions
Latest release: 11 months ago
10 dependent packages
8,317 downloads last month

Papers Mentioning ParmEd 23

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Cited by: 10
Author(s): Nikolina Šoštarić, Vera van Noort
Software Mentions: 5
Published: over 3 years ago

10.3389/fmolb.2021.720561

Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors
Cited by: 5
Author(s): Giuseppe Deganutti, Silvia Atanasio, Roxana Maria Rujan, Patrick M. Sexton, Denise Wootten, Christopher A. Reynolds
Software Mentions: 4
Published: about 3 years ago

10.1093/bioinformatics/bty347

Applying graph theory to protein structures: an Atlas of coiled coils
Cited by: 15
Author(s): Jack W. Heal, Gail J. Bartlett, Christopher W. Wood, Andrew Thomson, Derek N. Woolfson
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1005659

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Cited by: 1,367
Author(s): Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yulan Zhao, Kyle A. Beauchamp, Lee‐Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya Stern, Rafal Wiewiora, Bernard R. Brooks, Vijay S. Pande
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0205179

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana
Cited by: 10
Author(s): Rashmi R. Hazarika, Nikolina Šoštarić, Yi‐Feng Sun, Vera van Noort
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13321-020-00451-6

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial
Cited by: 9
Author(s): Simon Bray, Tharindu Senapathi, Christopher B. Barnett, Björn Grüning
Software Mentions: 4
Published: about 4 years ago

10.3390/biom11040529

Interaction of Ligands for PET with the Dopamine D3 Receptor: In Silico and In Vitro Methods
Cited by: 6
Author(s): Chia-Ju Hsieh, Aladdin Riad, Ji Youn Lee, Kristoffer Sahlholm, Kuiying Xu, Robert R. Luedtke, Robert H. Mach
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-47249-7

Differential binding affinity of tau repeat region R2 with neuronal-specific β-tubulin isotypes
Cited by: 13
Author(s): Vishwambhar Vishnu Bhandare, Bajarang Vasant Kumbhar, Ambarish Kunwar
Software Mentions: 3
Published: about 5 years ago

10.1098/rsfs.2019.0128

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors
Cited by: 9
Author(s): Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend‐Nicholson, Peter V. Coveney
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms22147288

Hybrid QM/MM Simulations Confirm Zn(II) Coordination Sphere That Includes Four Cysteines from the P2 × 4R Head Domain
Cited by: 1
Author(s): Francisco Andrés Peralta, J. Pablo Huidobro‐Toro, Raúl Mera‐Adasme
Software Mentions: 2
Published: about 3 years ago

10.12688/f1000research.14960.2

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules
Cited by: 5
Author(s): Guilherme Duarte Ramos Matos, David L. Mobley
Software Mentions: 2
Published: over 5 years ago

10.3389/fchem.2018.00650

Computational Study of Protein-Ligand Unbinding for Enzyme Engineering
Cited by: 30
Author(s): Sérgio M. Marques, David Bednář, Jiřı́ Damborský
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-72889-5

A structure-based computational workflow to predict liability and binding modes of small molecules to hERG
Cited by: 14
Author(s): Subha Kalyaanamoorthy, Shawn M. Lamothe, Xiaoqing Hou, Tae Chul Moon, Harley T. Kurata, Michael Houghton, Khaled Barakat
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-74099-5

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation
Cited by: 55
Author(s): Teruhisa Komatsu, Noriaki Okimoto, Yohei M. Koyama, Yoshinori Hirano, Gentaro Morimoto, Yosuke Ohno, Makoto Taiji
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms22073650

Unveiling the N-Terminal Homodimerization of BCL11B by Hybrid Solvent Replica-Exchange Simulations
Cited by: 2
Author(s): Lukas Schulig, Piotr Grabarczyk, Norman Geist, Martin Delin, Hannes Forkel, Martin Kulke, Mihaela Delcea, Christian A. Schmidt, Andreas Link
Software Mentions: 2
Published: over 3 years ago

10.1093/bioinformatics/btx037

Ligandbook: an online repository for small and drug-like molecule force field parameters
Cited by: 15
Author(s): Jan Domański, Oliver Beckstein, Bogdan I. Iorga
Software Mentions: 2
Published: over 7 years ago

10.3390/biom10121647

Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution
Cited by: 7
Author(s): Camille Samson, Pierre Legrand, Mustafa Tekpinar, Jef Rozenski, Mikhail Abramov, Philipp Holliger, Vitor B. Pinheiro, Piet Herdwijn, Marc Delarue
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-019-56078-7

Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2
Cited by: 3
Author(s): Dmitrii A. Luzik, Olga N. Rogacheva, Sergei A. Izmailov, Maria I. Indeykina, А. С. Кононихин, Nikolai R. Skrynnikov
Software Mentions: 1
Published: over 4 years ago

10.1021/acs.jmedchem.1c00533

Halting the Spread of Herpes Simplex Virus-1: The Discovery of an Effective Dual αvβ6/αvβ8 Integrin Ligand
Cited by: 8
Author(s): Stefano Tomassi, Vincenzo Maria D’Amore, Francesco Saverio Di Leva, Andrea Vannini, Giacomo Quilici, Michael Weinmüller, Florian Reichart, Jussara Amato, Barbara Romano, Angelo A. Izzo, Salvatore Di Maro, Ettore Novellino, Giovanna Musco, Tatiana Gianni, Horst Kessler, Luciana Marinelli
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2020.00106

On Calculating Free Energy Differences Using Ensembles of Transition Paths
Cited by: 29
Author(s): Robert M. Hall, Tom Dixon, Alex Dickson
Software Mentions: 1
Published: over 4 years ago

10.1161/CIRCULATIONAHA.121.053350

Cardiac Late Sodium Channel Current Is a Molecular Target for the Sodium/Glucose Cotransporter 2 Inhibitor Empagliflozin
Cited by: 88
Author(s): Koenraad Philippaert, Subha Kalyaanamoorthy, Mohammad Fatehi, Wentong Long, Shubham Soni, Nikole J. Byrne, Amy Barr, Jyoti Singh, Jordan Wong, Taylor Palechuk, Chloe Schneider, Ahmed M. Darwesh, Zaid H. Maayah, John M. Seubert, Khaled Barakat, Jason R.B. Dyck, Peter E. Light
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-017-00256-y

Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter
Cited by: 13
Author(s): Matthew P. Harrigan, Keri A. McKiernan, Veerabahu Shanmugasundaram, R. Aldrin Denny, Vijay S. Pande
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-09229-7

Simple MD-based model for oxidative folding of peptides and proteins
Cited by: 6
Author(s): Sergei A. Izmailov, Ivan S. Podkorytov, Nikolai R. Skrynnikov
Software Mentions: 1
Published: about 7 years ago