cran: AMOEBA | Projects | Ecosyste.ms: Papers

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: over 7 years ago

10.3390/ijms22179422

Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes
Cited by: 28
Author(s): Anna Mazurek, Łukasz Szeleszczuk, Tomasz Gubica
Software Mentions: 4
Published: about 3 years ago

10.1039/c7sc04531j

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields
Cited by: 183
Author(s): Louis Lagardère, Luc‐Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, Zhifeng Jing, Matthew Harger, Hedieh Torabifard, G. Andrés Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday, Pengyu Ren, Jay W. Ponder, Jean‐Philip Piquemal
Software Mentions: 3
Published: almost 7 years ago

10.1039/d1sc00145k

High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling
Cited by: 31
Author(s): Théo Jaffrelot Inizan, Frédéric Célerse, Olivier Adjoua, Dina El Ahdab, Luc‐Henri Jolly, Chengwen Liu, Pengyu Ren, Matthieu Montès, Nathalie Lagarde, Louis Lagardère, Pierre Monmarché, Jean‐Philip Piquemal
Software Mentions: 3
Published: almost 4 years ago

10.1107/S0907444909022707

Polarizable atomic multipole X-ray refinement: application to peptide crystals
Cited by: 48
Author(s): Michael J. Schnieders, Timothy D. Fenn, Vijay S. Pande, Axel T. Brunger
Software Mentions: 3
Published: over 15 years ago

10.1016/j.snb.2016.08.076

Automated microbeam observation environment for biological analysis—Custom portable environmental control applied to a vertical microbeam system
Cited by: 2
Author(s): Matthew J. England, Alan W. Bigelow, Michael J Merchant, Eirini Velliou, David Welch, David J. Brenner, K.J. Kirkby
Software Mentions: 2
Published: almost 8 years ago

10.3390/s19163589

A Survey of Security Services, Attacks, and Applications for Vehicular Ad Hoc Networks (VANETs)
Cited by: 106
Author(s): Muhammad Sameer Sheikh, Jun Liang, Wensong Wang
Software Mentions: 2
Published: over 5 years ago

10.3390/s19183926

Delaunay Triangulation-Based Spatial Clustering Technique for Enhanced Adjacent Boundary Detection and Segmentation of LiDAR 3D Point Clouds
Cited by: 15
Author(s): Jongwon Kim, Jeongho Cho
Software Mentions: 2
Published: about 5 years ago

10.3390/ijerph14030274

Utilizing Crowdsourced Data for Studies of Cycling and Air Pollution Exposure: A Case Study Using Strava Data
Cited by: 62
Author(s): Yeran Sun, Amin Mobasheri
Software Mentions: 2
Published: over 7 years ago

10.3389/fmolb.2019.00143

Accurate Biomolecular Simulations Account for Electronic Polarization
Cited by: 45
Author(s): Josef Melcr, Jean‐Philip Piquemal
Software Mentions: 2
Published: almost 5 years ago

10.1007/s00894-019-4095-3

The influence of water potential in simulation: a catabolite activator protein case study
Cited by: 5
Author(s): Steven Y. Liem, Paul L. A. Popelier
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21030697

Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic Liquids
Cited by: 23
Author(s): Erik Antonio Vázquez-Montelongo, José Enrique Vázquez-Cervantes, G. Andrés Cisneros
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21176339

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems
Cited by: 69
Author(s): Raudah Lazim, Donghyuk Suh, Sun Choi
Software Mentions: 2
Published: about 4 years ago

10.1039/c7sc00997f

Computational investigation of O<sub>2</sub>diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O<sub>2</sub>transport
Cited by: 25
Author(s): Hedieh Torabifard, G. Andrés Cisneros
Software Mentions: 2
Published: almost 8 years ago

10.1021/acs.jctc.1c00555

Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation
Cited by: 8
Author(s): Michele Nottoli, Riccardo Nifosı̀, Benedetta Mennucci, Filippo Lipparini
Software Mentions: 2
Published: about 3 years ago

10.1021/acs.jpcb.1c05753

Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics
Cited by: 7
Author(s): Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0123146

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics
Cited by: 25
Author(s): Daniel J. Kuster, Chengyu Liu, John Fang, Jay W. Ponder, Garland R. Marshall
Software Mentions: 2
Published: over 9 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: almost 6 years ago

10.3389/fchem.2018.00189

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein
Cited by: 5
Author(s): Mingyuan Xu, Tong Zhu, John Z. H. Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fmolb.2021.712085

Recent Developments in Free Energy Calculations for Drug Discovery
Cited by: 39
Author(s): Edward J. King, Erick Aitchison, Han Li, Ray Luo
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-018-31722-w

Parameter-Free Multiscale Simulation Realising Quantitative Prediction of Hole and Electron Mobilities in Organic Amorphous System with Multiple Frontier Orbitals
Cited by: 20
Author(s): Syozo Kubo, Hironori Kaji
Software Mentions: 1
Published: about 6 years ago

10.3390/ijerph18189848

Issues in the Current Practices of Spatial Cluster Detection and Exploring Alternative Methods
Cited by: 4
Author(s): David W. S. Wong
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms22073420

Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins
Cited by: 9
Author(s): Meili Liu, Akshaya Kumar Das, James Lincoff, Sukanya Sasmal, Sara Y. Cheng, Robert Vernon, Julie D. Forman-Kay, Teresa Head‐Gordon
Software Mentions: 1
Published: over 3 years ago

10.1002/jcc.26111

A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics
Cited by: 20
Author(s): Zak E. Hughes, Emmanuel Ren, Joseph C. R. Thacker, Benjamin C. B. Symons, Arnaldo F. Silva, Paul L. A. Popelier
Software Mentions: 1
Published: about 5 years ago

10.1186/s12886-020-01659-8

Nanophthalmos patient with a THR518MET mutation in MYRF, a case report
Cited by: 4
Author(s): Joshua Hagedorn, Armin Avdic, Michael J. Schnieders, Ben R. Roos, Young H. Kwon, Arlene V. Drack, Erin A. Boese, John H. Fingert
Software Mentions: 1
Published: about 4 years ago

10.3390/molecules23112830

Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF4]
Cited by: 11
Author(s): Erik Antonio Vázquez-Montelongo, José Enrique Vázquez-Cervantes, G. Andrés Cisneros
Software Mentions: 1
Published: about 6 years ago

10.3390/molecules23010077

A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids
Cited by: 8
Author(s): Huiying Chu, Xiangda Peng, Yan Li, Yuebin Zhang, Guohui Li
Software Mentions: 1
Published: almost 7 years ago

10.3390/molecules26175379

Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes
Cited by: 12
Author(s): Na Li, Ya Gao, Feng Qiu, Tong Zhu
Software Mentions: 1
Published: about 3 years ago

10.3390/molecules26113384

Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding
Cited by: 3
Author(s): Daria V. Berdnikova, Paolo Carloni, Sybille Krauß, Giulia Rossetti
Software Mentions: 1
Published: over 3 years ago

10.1039/c3cp54164a

Current and emerging opportunities for molecular simulations in structure-based drug design
Cited by: 43
Author(s): Julien Michel
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0122468

A Permeability Study of O2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers
Cited by: 12
Author(s): Bryan W. Holland, Mark D. Berry, C.G. Gray, Bruno Tomberli
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0202141

Tubulin's response to external electric fields by molecular dynamics simulations
Cited by: 20
Author(s): Joshua J. Timmons, Jordane Preto, Jack A. Tuszyński, Eric T. Wong
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0224991

Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator
Cited by: 4
Author(s): Yeyue Xiong, Alexey V. Onufriev
Software Mentions: 1
Published: about 5 years ago

10.1039/d1sc01276b

Vibrational exciton delocalization precludes the use of infrared intensities as proxies for surfactant accumulation on aqueous surfaces
Cited by: 2
Author(s): Kimberly A. Carter-Fenk, Kevin Carter-Fenk, Michelle Fiamingo, Heather C. Allen, John M. Herbert
Software Mentions: 1
Published: almost 4 years ago

10.1039/c9sc01745c

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings
Cited by: 46
Author(s): Daniele Loco, Louis Lagardère, G. Andrés Cisneros, Giovanni Scalmani, Michael J. Frisch, Filippo Lipparini, Benedetta Mennucci, Jean‐Philip Piquemal
Software Mentions: 1
Published: almost 6 years ago

10.3389/fchem.2020.00440

Quantum-Chemistry Based Design of Halobenzene Derivatives With Augmented Affinities for the HIV-1 Viral G4/C16 Base-Pair
Cited by: 2
Author(s): Perla El Darazi, Léa El Khoury, Krystel El Hage, Richard G. Maroun, Zeina Hobaika, Jean‐Philip Piquemal, Nohad Gresh
Software Mentions: 1
Published: over 4 years ago

10.3389/fmolb.2015.00009

Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis
Cited by: 14
Author(s): Qiantao Wang, Ramakrishna Edupuganti, Clint D.J. Tavares, Kevin N. Dalby, Pengyu Ren
Software Mentions: 1
Published: over 9 years ago

10.1002/jcc.24006

Realistic sampling of amino acid geometries for a multipolar polarizable force field
Cited by: 16
Author(s): T. Hughes, Salvatore Cardamone, Paul L. A. Popelier
Software Mentions: 1
Published: over 9 years ago

10.1002/jcc.24500

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field
Cited by: 31
Author(s): Noor Asidah Mohamed, Richard T. Bradshaw, Jonathan W. Essex
Software Mentions: 1
Published: about 8 years ago

10.1038/srep17421

Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation
Cited by: 36
Author(s): Jianzhong Chen, Jinan Wang, Qinggang Zhang, Kaixian Chen, Weiliang Zhu
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-16314-4

Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations
Cited by: 21
Author(s): Lina Kulakova, Georgios Arampatzis, Panagiotis Angelikopoulos, Panagiotis E. Hadjidoukas, Costas Papadimitriou, Petros Koumoutsakos
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-18012-7

Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane
Cited by: 19
Author(s): Qunzhi Zhu, Yue Lu, Xibing He, Tao Liu, Hongwei Chen, Fang Wang, Zheng Dong, Hao Dong, Jing Ma
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-25418-4

Chemical shift extremum of 129Xe(aq) reveals details of hydrophobic solvation
Cited by: 9
Author(s): Petri Peuravaara, Jouni Karjalainen, Jianfeng Zhu, Jiřı́ J. Mareš, Perttu Lantto, Juha Vaara
Software Mentions: 1
Published: over 6 years ago

Projects: cran: AMOEBA

Papers Mentioning AMOEBA 43