Ecosyste.ms: Papers

10.3390/ijms21207626

Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations
Cited 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 Complexes
Cited by: 28
Author(s): Anna Mazurek, Łukasz Szeleszczuk, Tomasz Gubica
Software Mentions: 4
Published: over 3 years ago

10.3762/bjoc.16.199

Computational tools for drawing, building and displaying carbohydrates: a visual guide
Cited 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 Mechanism
Cited 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 granules
Cited 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 selection
Cited 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 Application
Cited 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 System
Cited 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 Leishmaniasis
Cited 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 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

10.3390/ijms21207702

Three-Dimensional Structures of Carbohydrates and Where to Find Them
Cited 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 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

10.1002/ana.24073

<i>GRIN2B</i> mutations in west syndrome and intellectual disability with focal epilepsy
Cited 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 Proteins
Cited by: 41
Author(s): R. Sathyapriya, José M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappé
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pcbi.1008150

Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination
Cited 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: over 4 years ago

10.1371/journal.pcbi.1008676

Finding branched pathways in metabolic network via atom group tracking
Cited 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 Enzymes
Cited 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 inhibition
Cited 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 Systems
Cited by: 12
Author(s): Daniel D. Lewis, Fernando Villarreal, Fan Wu, Cheemeng Tan
Software Mentions: 2
Published: about 10 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: about 5 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: over 3 years ago

10.1186/1742-4682-3-1

Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b
Cited 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 epitopes
Cited 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: about 7 years ago

10.3390/ijms20020422

Towards Unraveling the Histone Code by Fragment Blind Docking
Cited 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 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

10.1021/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: over 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: over 6 years ago

10.5936/csbj.201308001

FREQUENCY OF DIPEPTIDES AND ANTIDIPEPTIDES
Cited 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 concolor
Cited 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 AML
Cited 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 block
Cited 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: almost 4 years ago

10.1186/1754-6834-5-71

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog
Cited 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 splitting
Cited 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 Simulations
Cited 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 amyloidoses
Cited 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 C1C2
Cited 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 oxidase
Cited by: 14
Author(s): Li‐Juan Yu, Emily Golden, Nanhao Chen, Yuan Zhao, Alice Vrielink, Amir Karton
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-74347-8

New insights on human IRE1 tetramer structures based on molecular modeling
Cited 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 ligands
Cited by: 4
Author(s): Sibo Lin, Jenna C. Fromer, Yagnaseni Ghosh, Brian S. Hanna, Mohamed Elanany, Wei Xu
Software Mentions: 1
Published: almost 4 years ago

10.3390/molecules22010008

Solvation Dynamics of CO2(g) by Monoethanolamine at the Gas–Liquid Interface: A Molecular Mechanics Approach
Cited 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 Analytics
Cited 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 Oligosaccharides
Cited 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 study
Cited 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 framework
Cited by: 15
Author(s): Khalid Ahmed Alzahrani, Robert J. Deeth
Software Mentions: 1
Published: almost 9 years ago

10.3390/antibiotics10091084

Microwave-Assisted, One-Pot Synthesis of Doxycycline under Heterogeneous Catalysis in Water
Cited 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: over 3 years ago

10.3390/molecules26164846

Incorporation of 4J-HMBC and NOE Data into Computer-Assisted Structure Elucidation with WebCocon
Cited 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 Fold
Cited by: 11
Author(s): Jianhui Feng, Mingfeng Li, Yanzhao Huang, Yi Xiao
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0168725

A Method for Finding Metabolic Pathways Using Atomic Group Tracking
Cited 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 Motif
Cited 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 surface
Cited 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-Review
Cited 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 structure
Cited 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 Cyclopeptide
Cited 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 accuracy
Cited 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 Switch
Cited 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