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: LigParGen
https://packages.ecosyste.ms/registries/pypi.org/packages/LigParGen
Python script to provide BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.
6 versions
Latest release: over 6 years ago
33 downloads last month
Papers Mentioning LigParGen 20
10.3390/ijms21207626
Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond ConformationsCited by: 4
Author(s): Viktor S. Stroylov, Maria V. Panova, Filip V. Toukach
Software Mentions: 5
Published: almost 4 years ago
10.3390/molecules26092430
Coumarin-Chalcone Hybrids as Inhibitors of MAO-B: Biological Activity and In Silico StudiesCited by: 14
Author(s): Guillermo Moya-Alvarado, Osvaldo Yáñez, Nicole Morales, Angélica González-González, Carlos Areche, Marco T. Núñez, Angélica Fierro, Olimpo García‐Beltrán
Software Mentions: 2
Published: over 3 years ago
10.1186/s13321-019-0348-5
QligFEP: an automated workflow for small molecule free energy calculations in QCited by: 46
Author(s): Willem Jespers, Mauricio Esguerra, Johan Åqvist, Hugo Gutiérrez‐de‐Terán
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0252571
Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2’s pathogenicity factorsCited by: 8
Author(s): Ömür Baysal, Naeem Abdul Ghafoor, Ragıp Soner Silme, А. Н. Игнатов, Volha Kniazeva
Software Mentions: 2
Published: over 3 years ago
10.1039/c8cs00040a
Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experimentsCited by: 109
Author(s): Pim W. J. M. Frederix, Ilias Patmanidis, Siewert J. Marrink
Software Mentions: 2
Published: over 6 years ago
10.3389/fchem.2019.00400
CherryPicker: An Algorithm for the Automated Parametrization of Large Biomolecules for Molecular SimulationCited by: 6
Author(s): Ivan D. Welsh, Jane R. Allison
Software Mentions: 2
Published: over 5 years ago
10.3389/fphar.2021.626735
Molecular Dynamics Studies of Therapeutic Liquid Mixtures and Their Binding to MycobacteriaCited by: 4
Author(s): Hugo P. Monteiro, Filipa Santos, Alexandre Paiva, Ana Rita C. Duarte, Ricardo B. Ferreira
Software Mentions: 2
Published: over 3 years ago
10.1007/s00894-021-04771-8
Electronic structure and reactivity of tirapazamine as a radiosensitizerCited by: 2
Author(s): José Romero, Thana Maihom, P. Limão-Vieira, Michael Probst
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms20235913
Model Optimization and In Silico Analysis of Potential Dipeptidyl Peptidase IV Antagonists from GC-MS Identified Compounds in Nauclea latifolia Leaf ExtractsCited by: 11
Author(s): Franklyn Nonso Iheagwam, Olubanke Olujoke Ogunlana, Shalom Nwodo Chinedu
Software Mentions: 1
Published: almost 5 years ago
10.3390/ijms21155391
Characterization of the Proteins Involved in the DNA Repair Mechanism in M. smegmatisCited by: 0
Author(s): Angela Di Somma, Carolina Canè, Antonio Moretta, Arianna Cirillo, Franz Cemič, Angela Duilio
Software Mentions: 1
Published: about 4 years ago
10.3390/molecules24244597
Investigation of Grignard Reagent as an Advanced Base for Aza-Claisen RearrangementCited by: 3
Author(s): Bo Song, Min Woo Ha, Dong Hwan Kim, Chanin Park, Keun Woo Lee, Seung‐Mann Paek
Software Mentions: 1
Published: almost 5 years ago
10.3390/polym12112764
Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen BondingCited by: 4
Author(s): Utkarsh Kapoor, Arjita Kulshreshtha, Arthi Jayaraman
Software Mentions: 1
Published: almost 4 years ago
10.3390/polym13111737
Two Fascinating Polysaccharides: Chitosan and Starch. Some Prominent Characterizations for Applying as Eco-Friendly Food Packaging and Pollutant Remover in Aqueous Medium. Progress in Recent Years: A ReviewCited by: 7
Author(s): Nancy Alvarado, Romina L. Abarca, Cristian Linares‐Flores
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-020-72113-4
Structure-based inhibitors targeting the alpha-helical domain of the Spiroplasma melliferum histone-like HU proteinCited by: 9
Author(s): Yuliya K. Agapova, Dmitry A. Altukhov, В. И. Тимофеев, Viktor S. Stroylov, Vitaly S. Mityanov, D.A. Korzhenevskiy, Anna V. Vlaskina, E. V. Smirnova, Eduard V. Bocharov, Tatiana V. Rakitina
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-021-84069-0
Ligand modulation of the conformational dynamics of the A2A adenosine receptor revealed by single-molecule fluorescenceCited by: 13
Author(s): Dennis D. Fernandes, Chris Neale, Gregory-Neal W. Gomes, Yuchong Li, Aqsa Malik, Akhilesh Pandey, Alexander P. Orazietti, Xudong Wang, Libin Ye, R. Scott Prosser, Claudiu C. Gradinaru
Software Mentions: 1
Published: over 3 years ago
10.3390/molecules25153424
The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics SimulationsCited by: 15
Author(s): Hugo A. L. Filipe, Maria João Moreno, Luís M. S. Loura
Software Mentions: 1
Published: about 4 years ago
10.3390/pharmaceutics13040531
Development of a Nanostructured Lipid Carrier (NLC) by a Low-Energy Method, Comparison of Release Kinetics and Molecular Dynamics SimulationCited by: 23
Author(s): Andrea C. Ortiz, Osvaldo Yáñez, Edison Salas-Huenuleo, Javier Morales
Software Mentions: 1
Published: over 3 years ago
10.1155/2020/1878410
Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal PlantsCited by: 8
Author(s): Franklyn Nonso Iheagwam, Solomon O. Rotimi
Software Mentions: 1
Published: about 4 years ago
10.3390/molecules26185482
Oxazinethione Derivatives as a Precursor to Pyrazolone and Pyrimidine Derivatives: Synthesis, Biological Activities, Molecular Modeling, ADME, and Molecular Dynamics StudiesCited by: 5
Author(s): Magda H. Abdellattif, Mohd Shahbaaz, M. M. H. Arief, Mostafa A. Hussien
Software Mentions: 1
Published: about 3 years ago
10.3390/e21080750
Entropy of Simulated Liquids Using Multiscale Cell CorrelationCited by: 16
Author(s): Hafiz Saqib Ali, Jonathan Higham, Richard H. Henchman
Software Mentions: 1
Published: about 5 years ago