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: Tinker
https://packages.ecosyste.ms/registries/pypi.org/packages/Tinker
1 version
Latest release: over 1 year ago
Papers Mentioning Tinker 55
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: about 4 years ago
10.3390/ijms22179422
Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin ComplexesCited by: 28
Author(s): Anna Mazurek, Łukasz Szeleszczuk, Tomasz Gubica
Software Mentions: 4
Published: about 3 years ago
10.3762/bjoc.16.199
Computational tools for drawing, building and displaying carbohydrates: a visual guideCited by: 12
Author(s): Kanhaya Lal, Rafael Bermeo, Serge Pérez
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pbio.1002146
The Structure of an NDR/LATS Kinase–Mob Complex Reveals a Novel Kinase–Coactivator System and Substrate Docking MechanismCited by: 45
Author(s): Gergő Gógl, Kyle D. Schneider, Brian J. Yeh, Alam Nashida, Alex N Nguyen Ba, Alan M. Moses, Csaba Hetényi, Attila Reményi, Eric L. Weiss
Software Mentions: 4
Published: over 9 years ago
10.7554/eLife.60833
Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granulesCited by: 9
Author(s): Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, Vinay K. Mayya, George Chung, Jia‐Xuan Chen, Hala Fahs, Yu Guan, Thomas F. Duchaîne, Matthias Selbach, Fabio Piano, Kristin C. Gunsalus
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0239609
Advancing crested wheatgrass [Agropyron cristatum (L.) Gaertn.] breeding through genotyping-by-sequencing and genomic selectionCited by: 4
Author(s): Kiran Baral, Bruce Coulman, Bill Biligetu, Yong‐Bi Fu
Software Mentions: 4
Published: about 4 years ago
10.3390/s21134258
Review: Development and Technical Design of Tangible User Interfaces in Wide-Field Areas of ApplicationCited by: 8
Author(s): Alice Krestanova, Martin Černý, Martin Augustýnek
Software Mentions: 3
Published: over 3 years ago
10.3390/s141121213
iMuseumA: An Agent-Based Context-Aware Intelligent Museum SystemCited by: 9
Author(s): Inmaculada Ayala, Mercedes Amor, Mónica Pinto, Lidia Fuentes, Nadia Gámez
Software Mentions: 3
Published: about 10 years ago
10.12688/f1000research.10701.2
Computational design of molecular motors as nanocircuits in LeishmaniasisCited by: 0
Author(s): Dipali Kosey, Shailza Singh
Software Mentions: 3
Published: over 7 years ago
10.1039/d1sc00145k
High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive samplingCited 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
10.3390/ijms21207702
Three-Dimensional Structures of Carbohydrates and Where to Find ThemCited by: 18
Author(s): Sofya I. Scherbinina, Filip V. Toukach
Software Mentions: 3
Published: about 4 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 fieldsCited 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
10.1002/ana.24073
<i>GRIN2B</i> mutations in west syndrome and intellectual disability with focal epilepsyCited by: 176
Author(s): Johannes R. Lemke, Rik Hendrickx, Kirsten Geider, Bodo Laube, Michael Schwake, Robert J. Harvey, Victoria M. James, Alex Pepler, Isabelle Steiner, Konstanze Hörtnagel, John Neidhardt, Susanne Ruf, Markus Wolff, Deborah Bartholdi, Roberto Caraballo, Konrad Platzer, Arvid Suls, Peter De Jonghe, Saskia Biskup, Sarah Weckhuysen
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pcbi.1000584
Defining an Essence of Structure Determining Residue Contacts in ProteinsCited by: 41
Author(s): R. Sathyapriya, José M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappé
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pcbi.1008150
Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determinationCited by: 4
Author(s): Yoonjoo Choi, Sukyo Jeong, Jungmin Choi, Christian Ndong, Karl E. Griswold, Chris Bailey‐Kellogg, Kwang Ho Kim
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pcbi.1008676
Finding branched pathways in metabolic network via atom group trackingCited by: 3
Author(s): Yiran Huang, Yusi Xie, Cheng Zhong, Fengfeng Zhou
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pcbi.1003714
A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 EnzymesCited by: 40
Author(s): Richard Lonsdale, Sarah L. Rouse, Mark S. P. Sansom, Adrian J. Mulholland
Software Mentions: 2
Published: over 10 years ago
10.1038/s42003-020-01184-w
Structural studies reveal flexible roof of active site responsible for ω-transaminase CrmG overcoming by-product inhibitionCited by: 8
Author(s): Jinxin Xu, Xiaowen Tang, Yiguang Zhu, Zhijun Yu, Kai Su, Yulong Zhang, Dong Yu, Weiming Zhu, Changsheng Zhang, Ruibo Wu, Jinsong Liu
Software Mentions: 2
Published: over 4 years ago
10.3389/fbioe.2014.00066
Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free SystemsCited by: 12
Author(s): Daniel D. Lewis, Fernando Villarreal, Fan Wu, Cheemeng Tan
Software Mentions: 2
Published: almost 10 years ago
10.3389/fmolb.2019.00143
Accurate Biomolecular Simulations Account for Electronic PolarizationCited by: 45
Author(s): Josef Melcr, Jean‐Philip Piquemal
Software Mentions: 2
Published: almost 5 years ago
10.1021/acs.jctc.1c00555
Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO ImplementationCited by: 8
Author(s): Michele Nottoli, Riccardo Nifosı̀, Benedetta Mennucci, Filippo Lipparini
Software Mentions: 2
Published: about 3 years ago
10.1186/1742-4682-3-1
Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2bCited by: 103
Author(s): Trevor G Marshall, Robert E. Lee, Frances Marshall
Software Mentions: 2
Published: almost 19 years ago
10.7554/eLife.29023
Computationally-driven identification of antibody epitopesCited by: 34
Author(s): Casey K. Hua, Albert T Gacerez, Charles L. Sentman, Margaret E. Ackerman, Yoonjoo Choi, Chris Bailey‐Kellogg
Software Mentions: 2
Published: almost 7 years ago
10.3390/ijms20020422
Towards Unraveling the Histone Code by Fragment Blind DockingCited by: 7
Author(s): Mónika Bálint, István Horváth, Nikolett Mészáros, Csaba Hetényi
Software Mentions: 2
Published: almost 6 years ago
10.3390/ijms21030697
Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic LiquidsCited by: 23
Author(s): Erik Antonio Vázquez-Montelongo, José Enrique Vázquez-Cervantes, G. Andrés Cisneros
Software Mentions: 2
Published: almost 5 years ago
10.1021/acs.jpcb.1c05753
Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM DynamicsCited by: 7
Author(s): Veronica Macaluso, Shaima Hashem, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci
Software Mentions: 2
Published: about 3 years ago
10.3390/ijms19092587
Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]Cited by: 12
Author(s): Kiran Baral, Bruce Coulman, Bill Biligetu, Yong‐Bi Fu
Software Mentions: 1
Published: about 6 years ago
10.5936/csbj.201308001
FREQUENCY OF DIPEPTIDES AND ANTIDIPEPTIDESCited by: 3
Author(s): Oliviero Carugo
Software Mentions: 1
Published: over 11 years ago
10.3390/molecules24142599
Nervisides I–J: Unconventional Side-Chain-Bearing Cycloartane Glycosides from Nervilia concolorCited by: 4
Author(s): Thi-Ngoc-Mai Tran, Guillaume Bernadat, Dinh-Tri Mai, Van-Kieu Nguyen, Jirapast Sichaem, Tan-Phat Nguyen, Cong-Luan Tran, Phuong-Vy Do, Ting An, Huu-Hung Nguyen, Mehdi A. Beniddir, Thuc‐Huy Duong, Pierre Le Pogam
Software Mentions: 1
Published: over 5 years ago
10.18632/oncotarget.8675
Dual inhibition of AKT/FLT3-ITD by A674563 overcomes FLT3 ligand-induced drug resistance in FLT3-ITD positive AMLCited by: 21
Author(s): Aoli Wang, Hong Wu, Chen Cheng, Changwei Hu, Qi Zhou, Qianqian Wang, Kewei Yu, Xiaochuan Liu, Fengming Zou, Zheng Zhao, Jiaxin Wu, Juan Liu, Feiyang Liu, Li Wang, Richard Stone, Ilene A. Galinksy, James D. Griffin, Shanchun Zhang, Ellen Weisberg, Jing Liu, Qingsong Liu
Software Mentions: 1
Published: over 8 years ago
10.1016/j.jsb.2020.107677
Direct transfer of electron microscopy samples to wetted carbon and graphene films via a support floatation blockCited by: 5
Author(s): Natàlia de Martín Garrido, Wencheng Fu, Kailash Ramlaul, Zining Zhu, Donald S. Miller, Daniel Boehringer, C.H.S. Aylett
Software Mentions: 1
Published: over 3 years ago
10.1186/1754-6834-5-71
Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analogCited by: 80
Author(s): Timothy J. Tschaplinski, Robert F. Standaert, Nancy L. Engle, Madhavi Z. Martin, Amandeep K. Sangha, Jerry M. Parks, Jeremy C. Smith, Reichel Samuel, Nan Jiang, Yunqiao Pu, Arthur J. Ragauskas, Choo Hamilton, Chunxiang Fu, Zeng‐Yu Wang, Brian H. Davison, Richard A. Dixon, Jonathan R. Mielenz
Software Mentions: 1
Published: almost 13 years ago
10.1098/rspa.2016.0138
Efficient molecular dynamics using geodesic integration and solvent–solute splittingCited by: 58
Author(s): Benedict Leimkuhler, Charles H. Matthews
Software Mentions: 1
Published: over 8 years ago
10.1038/srep26264
HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular SimulationsCited by: 9
Author(s): Chunyang Yu, Lingling Ma, Shanlong Li, Haina Tan, Yongfeng Zhou, Deyue Yan
Software Mentions: 1
Published: over 8 years ago
10.1038/srep36631
A scFv antibody targeting common oligomeric epitope has potential for treating several amyloidosesCited by: 27
Author(s): Jun Zha, Xiang‐meng Liu, Jie Zhu, Shuying Liu, Shan Lü, Peng‐xin Xu, Xiaolin Yu, Rui‐tian Liu
Software Mentions: 1
Published: about 8 years ago
10.1038/s41598-017-07363-w
Reaction dynamics of the chimeric channelrhodopsin C1C2Cited by: 44
Author(s): Yusaku Hontani, Marco Marazzi, Katja Stehfest, Tilo Mathes, Ivo H. M. van Stokkum, Marcus Elstner, Peter Hegemann, John T. M. Kennis
Software Mentions: 1
Published: over 7 years ago
10.1038/s41598-017-17503-x
Computational insights for the hydride transfer and distinctive roles of key residues in cholesterol oxidaseCited by: 14
Author(s): Li‐Juan Yu, Emily Golden, Nanhao Chen, Yuan Zhao, Alice Vrielink, Amir Karton
Software Mentions: 1
Published: almost 7 years ago
10.1038/s41598-020-74347-8
New insights on human IRE1 tetramer structures based on molecular modelingCited by: 4
Author(s): Antonio Carlesso, Johanna Hörberg, Anna Reymer, Leif A. Eriksson
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-021-82816-x
Computer-assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligandsCited by: 4
Author(s): Sibo Lin, Jenna C. Fromer, Yagnaseni Ghosh, Brian S. Hanna, Mohamed Elanany, Wei Xu
Software Mentions: 1
Published: over 3 years ago
10.3390/molecules22010008
Solvation Dynamics of CO2(g) by Monoethanolamine at the Gas–Liquid Interface: A Molecular Mechanics ApproachCited by: 7
Author(s): I-Shou Huang, Jia-Jen Li, Ming Kang Tsai
Software Mentions: 1
Published: almost 8 years ago
10.3390/s19153291
Introducing Low-Cost Sensors into the Classroom Settings: Improving the Assessment in Agile Practices with Multimodal Learning AnalyticsCited by: 19
Author(s): Héctor Cornide-Reyes, René Noël, Fabián Riquelme, Matías Gajardo, Cristian Cechinel, Roberto Mac Lean, Carlos Becerra, Rodolfo Villarroel, Roberto Castro-Muñoz
Software Mentions: 1
Published: over 5 years ago
10.3390/molecules26092418
Stochastic Modelling of 13C NMR Spin Relaxation Experiments in OligosaccharidesCited by: 1
Author(s): Sergio Rampino, Mirco Zerbetto, Antonino Polimeno
Software Mentions: 1
Published: over 3 years ago
10.1042/BJ20141211
Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis studyCited by: 81
Author(s): Dolores Linde, Rebecca Pogni, Marina Cañellas, Fátima Lucas, Vı́ctor Guallar, Maria Camilla Baratto, Adalgisa Sinicropi, Verónica Sáez-Jiménez, Cristina Coscolín, Antonio Romero, F.J. Medrano, Francisco J. Ruiz‐Dueñas, Ángel T. Martínez
Software Mentions: 1
Published: almost 10 years ago
10.1007/s00894-016-2949-5
Molecular modeling of zinc paddlewheel molecular complexes and the pores of a flexible metal organic frameworkCited by: 15
Author(s): Khalid Ahmed Alzahrani, Robert J. Deeth
Software Mentions: 1
Published: over 8 years ago
10.3390/antibiotics10091084
Microwave-Assisted, One-Pot Synthesis of Doxycycline under Heterogeneous Catalysis in WaterCited by: 1
Author(s): Fabio Bucciol, Elia Maffeis, Emanuela Calcio Gaudino, László Jicsinszky, Silvia Tagliapietra, Alessandro Barge, Cristina Prandi, Giancarlo Cravotto
Software Mentions: 1
Published: about 3 years ago
10.3390/molecules26164846
Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCoconCited by: 5
Author(s): Matthias Köck, Thomas Lindel, J. Junker
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0014138
Symmetric Key Structural Residues in Symmetric Proteins with Beta-Trefoil FoldCited by: 11
Author(s): Jianhui Feng, Mingfeng Li, Yanzhao Huang, Yi Xiao
Software Mentions: 1
Published: almost 14 years ago
10.1371/journal.pone.0168725
A Method for Finding Metabolic Pathways Using Atomic Group TrackingCited by: 21
Author(s): Yiran Huang, Cheng Zhong, Hai Lin, Jianyi Wang
Software Mentions: 1
Published: almost 8 years ago
10.3390/vaccines9070754
Epitope–Paratope Interaction of a Neutralizing Human Anti-Hepatitis B Virus PreS1 Antibody That Recognizes the Receptor-Binding MotifCited by: 0
Author(s): Jisu Hong, Young–Jin Choi, Yoonjoo Choi, Jiwoo Lee, Hyo Jeong Hong
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0177740
Fast exploration of an optimal path on the multidimensional free energy surfaceCited by: 1
Author(s): Changjun Chen
Software Mentions: 1
Published: over 7 years ago
10.3390/molecules24091653
Molecular Simulations with in-deMon2k QM/MM, a Tutorial-ReviewCited by: 26
Author(s): Aurélien de la Lande, Aurélio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, Patrizia Calaminici, L. López-Sosa, Gerald Geudtner, Isabelle Navizet, Cristina García‐Iriepa, Dennis R. Salahub, Andreas M. Köster
Software Mentions: 1
Published: over 5 years ago
10.1039/d0sc00442a
DP4-AI automated NMR data analysis: straight from spectrometer to structureCited by: 79
Author(s): Alexander Howarth, Kristaps Ermanis, Jonathan M. Goodman
Software Mentions: 1
Published: almost 5 years ago
10.3390/molecules25040922
Structure-Based Design, Synthesis and Bioactivity of a New Anti-TNFα CyclopeptideCited by: 9
Author(s): Mohannad Idress, Bruce F. Milne, Gary S. Thompson, Laurent Trembleau, Marcel Jaspars, Wael E. Houssen
Software Mentions: 1
Published: almost 5 years ago
10.1039/c5sc03014e
Predicting finite-temperature properties of crystalline carbon dioxide from first principles with quantitative accuracyCited by: 58
Author(s): Yonaton N. Heit, Kaushik Nanda, Gregory J. O. Beran
Software Mentions: 1
Published: almost 9 years ago
10.1002/chem.202001566
Tuning Aqueous Supramolecular Polymerization by an Acid‐Responsive Conformational SwitchCited by: 9
Author(s): Christina Rest, Divya Susan Philips, Torsten Dünnebacke, Papri Sutar, Ángel Sampedro, Jörn Droste, Vladimir Stepanenko, Michael Ryan Hansen, Rodrigo Q. Albuquerque, Gustavo Fernández
Software Mentions: 1
Published: over 4 years ago