pypi: MDAnalysis | Projects | Ecosyste.ms: Papers

10.1016/j.jmb.2013.10.024

Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY
Cited by: 63
Author(s): Lukas S. Stelzl, Philip W. Fowler, Mark S. P. Sansom, Oliver Beckstein
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.65545

Dwarf open reading frame (DWORF) is a direct activator of the sarcoplasmic reticulum calcium pump SERCA
Cited by: 28
Author(s): M'Lynn E Fisher, Elisa Bovo, Rodrigo Aguayo‐Ortiz, Ellen E. Cho, Marsha P. Pribadi, Michael P. Dalton, Nishadh Rathod, M. Joanne Lemieux, L. Michel Espinoza-Fonseca, Seth L. Robia, Aleksey V. Zima, Howard S. Young
Software Mentions: 2
Published: over 3 years ago

10.1016/j.cell.2021.01.037

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Cited by: 508
Author(s): Emma C. Thomson, Laura E. Rosen, James G. Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A. Wojcechowskyj, Chris Davis, Luca Piccoli, David Pascall, Josh R Dillen, Spyros Lytras, Nadine Czudnochowski, Rajiv Shah, Marcel Meury, Natasha Jesudason, Anna De Marco, Kathy Li, Jessica Bassi, Áine O’Toole, Dora Pinto, Rachel Colquhoun, Katja Culap, Ben Jackson, Fabrizia Zatta, Andrew Rambaut, Stefano Jaconi, Vattipally B Sreenu, Jay C. Nix, Ivy Zhang, Ruth F. Jarrett, William G. Glass, Martina Beltramello, Kyriaki Nomikou, Matteo Samuele Pizzuto, L. Tong, Elisabetta Cameroni, Tristan I. Croll, Natasha Johnson, Julia di Iulio, Arthur Wickenhagen, Alessandro Ceschi, Aoife M Harbison, Daniel Mair, Paolo Ferrari, Katherine Smollett, Federica Sallusto, Stephen Carmichael, Christian Garzoni, Jenna Nichols, Massimo Galli, Joseph Hughes, Agostino Riva, Antonia Ho, Marco Schiuma, Malcolm G Semple, Peter Openshaw, Elisa Fadda, J Kenneth Baillie, John D. Chodera, Suzannah J. Rihn, Samantha Lycett, Herbert W. Virgin, Amalio Telenti, Davide Corti, David L. Robertson, Gyorgy Snell
Software Mentions: 2
Published: over 3 years ago

10.1007/s00018-019-03211-4

Discovering the chloride pathway in the CFTR channel
Cited by: 14
Author(s): Bianka Farkas, Hedvig Tordai, Rita Padányi, Attila Tordai, János Gera, Gábor Paragi, Tamás Hegedüs
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms19092772

Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study
Cited by: 3
Author(s): Jean-Marc Crowet, Mehmet Nail Nasir, Nicolas Dony, Antoine Deschamps, Vincent Stroobant, Pierre Morsomme, Magali Deleu, Patrice Soumillion, Laurence Lins
Software Mentions: 2
Published: about 6 years ago

10.1016/j.bbamem.2016.02.007

Computational virology: From the inside out
Cited by: 44
Author(s): Tyler Reddy, Mark S. P. Sansom
Software Mentions: 2
Published: about 8 years ago

10.1016/j.jsb.2019.107405

Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain
Cited by: 6
Author(s): Salomé Llabrés, Maxim I. Tsenkov, Stuart A. MacGowan, Geoffrey J. Barton, Ulrich Zachariae
Software Mentions: 1
Published: over 4 years ago

10.1007/s12010-021-03601-0

Computational Resources for Bioscience Education
Cited by: 0
Author(s): Rup Kumar Kar
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-017-1506-2

Classifying kinase conformations using a machine learning approach
Cited by: 34
Author(s): Daniel McSkimming, Khaled Rasheed, Natarajan Kannan
Software Mentions: 1
Published: over 7 years ago

10.1186/s12900-018-0083-6

re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling
Cited by: 6
Author(s): Gilles Lamothe, Thérèse E. Malliavin
Software Mentions: 1
Published: over 6 years ago

10.3762/bjnano.11.74

Three-dimensional solvation structure of ethanol on carbonate minerals
Cited by: 6
Author(s): Hagen Söngen, Ygor Morais Jaques, Peter Spijker, Christoph Marutschke, Stefanie Klassen, Ilka Hermes, Ralf Bechstein, Lidija Zivanovic, John Tracey, Adam S. Foster, Angelika Kühnle
Software Mentions: 1
Published: over 4 years ago

10.1016/j.bbagen.2016.07.020

Understanding the role of dynamics in the iron sulfur cluster molecular machine
Cited by: 17
Author(s): Danilo Di Maio, Balasubramanian Chandramouli, Robert Yan, Giuseppe Brancato, Annalisa Pastore
Software Mentions: 1
Published: over 7 years ago

10.1016/j.bpj.2019.10.028

tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition
Cited by: 16
Author(s): Malte Warias, Helmut Grubmüller, Lars V. Bock
Software Mentions: 1
Published: over 4 years ago

10.3390/life11020074

Qualitative Prediction of Ligand Dissociation Kinetics from Focal Adhesion Kinase Using Steered Molecular Dynamics
Cited by: 11
Author(s): Justin Spiriti, Chung F. Wong
Software Mentions: 1
Published: over 3 years ago

10.3390/membranes11060410

Synergistic Effect of Chemical Penetration Enhancers on Lidocaine Permeability Revealed by Coarse-Grained Molecular Dynamics Simulations
Cited by: 3
Author(s): Marine E. Bozdaganyan, Philipp Orekhov
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules26164955

Identification and In Silico Characterization of Novel Helicobacter pylori Glucose-6-Phosphate Dehydrogenase Inhibitors
Cited by: 4
Author(s): Beatriz Hernández-Ochoa, Gabriel Navarrete‐Vázquez, Rodrigo Aguayo‐Ortiz, Paulina Ortiz-Ramírez, Laura Morales-Luna, Víctor Martínez‐Rosas, Abigail González‐Valdez, Fernando Gómez‐Chávez, Sergio Enríquez-Flores, Carlos Wong-Baeza, Isabel Baeza-Ramírez, Verónica Pérez de la Cruz, Saúl Gómez-Manzo
Software Mentions: 1
Published: about 3 years ago

10.3390/molecules25081848

PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations
Cited by: 5
Author(s): Pedro A. Sánchez, Martin Vögele, Jens Smiatek, Botao Qiao, Marcello Sega, Christian Holm
Software Mentions: 1
Published: over 4 years ago

10.3390/molecules24091756

Triazolopeptides Inhibiting the Interaction between Neuropilin-1 and Vascular Endothelial Growth Factor-165
Cited by: 12
Author(s): Bartłomiej Fedorczyk, Piotr F. J. Lipiński, Anna K. Puszko, Dagmara Tymecka, Beata Wileńska, Wioleta Dudka, G Perret, Rafał Wieczorek, Aleksandra Misicka
Software Mentions: 1
Published: over 5 years ago

10.1007/s00706-016-1674-1

Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations
Cited by: 15
Author(s): Marcus Wieder, Ugo Perricone, Thomas Seidel, Stefan Boresch, Thierry Langer
Software Mentions: 1
Published: over 8 years ago

10.3390/v13071395

Modeling of CCR5 Recognition by HIV-1 gp120: How the Viral Protein Exploits the Conformational Plasticity of the Coreceptor
Cited by: 9
Author(s): Célien Jacquemard, Florian Koensgen, Philippe Colin, Bernard Lagane, Esther Kellenberger
Software Mentions: 1
Published: about 3 years ago

10.7717/peerj.4143

Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages
Cited by: 7
Author(s): Galya V. Klink, Andrey V. Golovin, Georgii A. Bazykin
Software Mentions: 1
Published: almost 7 years ago

10.1039/c7cp07052g

Solvation dynamics in polar solvents and imidazolium ionic liquids: failure of linear response approximations
Cited by: 22
Author(s): Esther Heid, Christian Schröder
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pcbi.1005880

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Cited by: 47
Author(s): Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1007056

The breadth of HIV-1 neutralizing antibodies depends on the conservation of key sites in their epitopes
Cited by: 15
Author(s): Hongjun Bai, Yifan Li, Nelson L. Michael, Merlin L. Robb, Morgane Rolland
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1004255

Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level
Cited by: 10
Author(s): Wanling Song, Harsha Bajaj, Chady Nasrallah, Hualiang Jiang, Mathias Winterhalter, J.P. Colletier, Yechun Xu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pcbi.1005240

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model
Cited by: 48
Author(s): Kristen A. Marino, Diego Prada‐Gracia, Davide Provasi, Marta Filizola
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pcbi.1006103

Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations
Cited by: 37
Author(s): Russell B. Davidson, Josie Hendrix, Brian J. Geiss, Martin McCullagh
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0191138

Interactions of 2’-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site
Cited by: 2
Author(s): Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0146066

Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR
Cited by: 14
Author(s): Dániel Szöllősi, Áron Erdei, Gergely Gyimesi, Csaba Magyar, Tamás Hegedüs
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0112419

A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex
Cited by: 87
Author(s): Kota Kasahara, Ikuo Fukuda, Haruki Nakamura
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0165208

Campomanesia adamantium Peel Extract in Antidiarrheal Activity: The Ability of Inhibition of Heat-Stable Enterotoxin by Polyphenols
Cited by: 24
Author(s): Caroline Honaiser Lescano, Ivan Pires de Oliveira, Tiago Zaminelli, Débora da Silva Baldivia, Luan Ramos da Silva, Mauro Napolitano, Camila Bitencourt Mendes Silvério, Nilton Lincopán, Eliana Janet Sanjinez-Argandoña
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0057990

Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges
Cited by: 254
Author(s): Zhihan Lv, Alex Tek, Franck Da Silva, Charly Empereur-mot, Matthieu Chavent, Marc Baaden
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0140258

Pathways and Barriers for Ion Translocation through the 5-HT3A Receptor Channel
Cited by: 20
Author(s): Danilo Di Maio, Balasubramanian Chandramouli, Giuseppe Brancato
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0156313

Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A
Cited by: 12
Author(s): David Gau, William Veon, Xuemei Zeng, Nathan A. Yates, Sanjeev G. Shroff, David Ryan Koes, Partha Roy
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0127034

Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents
Cited by: 31
Author(s): Hailey R. Bureau, Dale R. Merz, Eli Hershkovits, Stephen Quirk, Rigoberto Hernandez
Software Mentions: 1
Published: over 9 years ago

10.1016/j.chembiol.2018.03.004

The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix
Cited by: 27
Author(s): Mehmet Gundogdu, Salomé Llabrés, Andrii Gorelik, Andrew T. Ferenbach, Ulrich Zachariae, Daan M. F. van Aalten
Software Mentions: 1
Published: over 6 years ago

10.1039/d0sc02164d

The rupture mechanism of rubredoxin is more complex than previously thought
Cited by: 1
Author(s): Maximilian Scheurer, Andreas Dreuw, Martin Head‐Gordon, Tim Stauch
Software Mentions: 1
Published: over 4 years ago

10.1039/d1sc01929e

Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8
Cited by: 5
Author(s): Vaibhav Kumar Shukla, Lucas Siemons, Francesco Luigi Gervasio, D. Flemming Hansen
Software Mentions: 1
Published: over 3 years ago

10.1038/s42003-021-01782-2

Specific PIP2 binding promotes calcium activation of TMEM16A chloride channels
Cited by: 18
Author(s): Zhiguang Jia, Jianhan Chen
Software Mentions: 1
Published: over 3 years ago

10.15252/embj.201387557

Molecular mechanism of ligand recognition by membrane transport protein, Mhp1
Cited by: 62
Author(s): Katie J. Simmons, Scott M. Jackson, Florian Brueckner, Simon G. Patching, Oliver Beckstein, Е. М. Иванова, Tao Geng, Simone Weyand, David Drew, Joseph Lanigan, David Sharples, Mark S. P. Sansom, So Iwata, Colin W. G. Fishwick, A. Peter Johnson, Alexander D. Cameron, Peter J. F. Henderson
Software Mentions: 1
Published: about 10 years ago

10.1140/epje/s10189-021-00119-5

AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations
Cited by: 2
Author(s): Sara Capponi, Shangying Wang, Erik J. Navarro, Simone Bianco
Software Mentions: 1
Published: almost 3 years ago

10.3389/fcimb.2021.729981

Conformation of the Solute-Binding Protein AdcAII Influences Zinc Uptake in Streptococcus pneumoniae
Cited by: 4
Author(s): M. Zupan, Zhenyao Luo, Katherine Ganio, Victoria G. Pederick, Stephanie L. Neville, Evelyne Deplazes, Boštjan Kobe, Christopher A. McDevitt
Software Mentions: 1
Published: about 3 years ago

10.3389/fchem.2021.716294

Role of Host-Guest Interaction in Understanding Polymerisation in Metal-Organic Frameworks
Cited by: 3
Author(s): A. D. Dinga Wonanke, Poppy Bennett, Lewis Caldwell, Matthew A. Addicoat
Software Mentions: 1
Published: about 3 years ago

10.3389/fchem.2021.704160

Transmembrane Self-Assembled Cyclic Peptide Nanotubes Based on α‐Residues and Cyclic δ‐Amino Acids: A Computational Study
Cited by: 3
Author(s): Alexandre Blanco-González, Martín Calvelo, Pablo F. Garrido, Manuel Amorín, Juan R. Granja, Ángel Piñeiro, Rebeca García‐Fandiño
Software Mentions: 1
Published: about 3 years ago

10.3389/fmolb.2021.707661

Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics
Cited by: 5
Author(s): Mahdi Hassankalhori, Giovanni Bolcato, Maicol Bissaro, Mattia Sturlese, Stefano Moro
Software Mentions: 1
Published: about 3 years ago

10.3389/fmolb.2021.676235

Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs
Cited by: 4
Author(s): Matteo Lambrughi, Emiliano Maiani, Burcu Aykaç Fas, Gary S. Shaw, Birthe B. Kragelund, Kresten Lindorff‐Larsen, Kaare Teilum, Gaetano Invernizzi, Elena Papaleo
Software Mentions: 1
Published: about 3 years ago

10.3389/fmolb.2020.591381

Properties of Cavities in Biological Structures—A Survey of the Protein Data Bank
Cited by: 9
Author(s): Mateusz Chwastyk, Ewa Panek, J. Malinowski, M. Jaskólski, Marek Cieplak
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmolb.2021.644644

Molecular Basis of Class B GPCR Selectivity for the Neuropeptides PACAP and VIP
Cited by: 13
Author(s): Chenyi Liao, Jacob M. Remington, Víctor May, Jianing Li
Software Mentions: 1
Published: over 3 years ago

10.3389/fmolb.2021.689400

Thermodynamic Origin of Differential Excipient-Lysozyme Interactions
Cited by: 7
Author(s): Jas Kalayan, Robin Curtis, Jim Warwicker, Richard H. Henchman
Software Mentions: 1
Published: over 3 years ago

10.1021/acs.jctc.1c00127

Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study
Cited by: 7
Author(s): Sebastian Franco-Ulloa, Daniela Guarnieri, Laura Riccardi, Pier Paolo Pompa, Marco De Vivo
Software Mentions: 1
Published: over 3 years ago

10.1186/s13321-020-00442-7

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform
Cited by: 15
Author(s): Simon Bray, Xavier Lucas, Anup Kumar, Björn Grüning
Software Mentions: 1
Published: over 4 years ago

10.3390/polym9100488

Cluster Formation of Polyphilic Molecules Solvated in a DPPC Bilayer
Cited by: 2
Author(s): Xiangyang Guo, Christopher Peschel, Tobias Watermann, Guido Falk von Rudorff, Daniel Sebastiani
Software Mentions: 1
Published: almost 7 years ago

10.3390/polym9090445

Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7)
Cited by: 1
Author(s): Christopher Peschel, Martin Brehm, Daniel Sebastiani
Software Mentions: 1
Published: about 7 years ago

10.3390/polym11122056

Grafting-Induced Structural Ordering of Lactide Chains
Cited by: 10
Author(s): Artyom D. Glova, Sofya D. Melnikova, Anna A. Mercurieva, Sergey V. Larin
Software Mentions: 1
Published: almost 5 years ago

10.1073/pnas.2019140117

Natural hybrid silica/protein superstructure at atomic resolution
Cited by: 15
Author(s): Stefan Görlich, A.J. Samuel, Richard J. Best, R.D. Seidel, Jean Vacelet, Filip Leonarski, Takashi Tanaka, Bernd Rellinghaus, Darius Pohl, Igor Zlotnikov
Software Mentions: 1
Published: almost 4 years ago

10.1073/pnas.2100425118

Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike
Cited by: 113
Author(s): Ahmad Reza Mehdipour, Gerhard Hummer
Software Mentions: 1
Published: over 3 years ago

10.1098/rsos.192208

Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes
Cited by: 13
Author(s): Ryan Bradley, David R. Slochower, Paul A. Janmey, Ravi Radhakrishnan
Software Mentions: 1
Published: over 4 years ago

10.1126/sciadv.aay5999

Streptavidin/biotin: Tethering geometry defines unbinding mechanics
Cited by: 59
Author(s): Steffen M. Sedlak, Leonard C. Schendel, Hermann E. Gaub, Rafael C. Bernardi
Software Mentions: 1
Published: over 4 years ago

10.1038/srep28164

Collapse of a lipid-coated nanobubble and subsequent liposome formation
Cited by: 24
Author(s): Kenichiro Koshiyama, Shigeo Wada
Software Mentions: 1
Published: over 8 years ago

10.1038/srep29634

A cholesterol-binding domain in STIM1 modulates STIM1-Orai1 physical and functional interactions
Cited by: 41
Author(s): Jonathan Pacheco, Laura Domı́nguez, Arlette Bohórquez-Hernández, Alexander Asanov, Luis Vaca
Software Mentions: 1
Published: about 8 years ago

10.1038/srep41515

Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains
Cited by: 22
Author(s): Manuel Hora, Martín Carballo-Pacheco, Benedikt Weber, Vanessa K. Morris, Antje Wittkopf, Johannes Büchner, Birgit Strodel, Bernd Reif
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-03745-2

Molecular dynamics exploration of poration and leaking caused by Kalata B1 in HIV-infected cell membrane compared to host and HIV membranes
Cited by: 11
Author(s): Wanapinun Nawae, Supa Hannongbua, Marasri Ruengjitchatchawalya
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37066-9

High-resolution experimental and computational electrophysiology reveals weak β-lactam binding events in the porin PorB
Cited by: 13
Author(s): Annika Bartsch, Salomé Llabrés, Florian Pein, Christof Kattner, Markus Schön, Manuel Diehn, Mikio Tanabe, Axel Munk, Ulrich Zachariae, Claudia Steinem
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-37814-x

Interplay between lipid lateral diffusion, dye concentration and membrane permeability unveiled by a combined spectroscopic and computational study of a model lipid bilayer
Cited by: 27
Author(s): Muhammad Jan Akhunzada, Francesca D’Autilia, Balasubramanian Chandramouli, Nicholus Bhattacharjee, Andrea Catte, Roberto Di Rienzo, Francesco Cardarelli, Giuseppe Brancato
Software Mentions: 1
Published: over 5 years ago

10.1039/c6sm01186a

Membrane stiffness is modified by integral membrane proteins
Cited by: 83
Author(s): Philip W. Fowler, Jean Hélie, Anna L. Duncan, Matthieu Chavent, Heidi Koldsø, Mark S. P. Sansom
Software Mentions: 1
Published: over 8 years ago

10.1186/s13029-015-0033-7

Membrainy: a ‘smart’, unified membrane analysis tool
Cited by: 26
Author(s): Matthew Carr, Cait E. MacPhee
Software Mentions: 1
Published: over 9 years ago

10.1016/j.jmb.2017.09.008

Effects of Periplasmic Chaperones and Membrane Thickness on BamA-Catalyzed Outer-Membrane Protein Folding
Cited by: 60
Author(s): Bob Schiffrin, Antonio N. Calabrese, A.J. Higgins, Julia R. Humes, Alison E. Ashcroft, Antreas C. Kalli, David J. Brockwell, Sheena E. Radford
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.52012

A molecular view on the escape of lipoplexed DNA from the endosome
Cited by: 35
Author(s): Bart Marlon Herwig Bruininks, Paulo C. T. Souza, Helgi I. Ingólfsson, Siewert J. Marrink
Software Mentions: 1
Published: over 4 years ago

10.7554/eLife.51212

The ion selectivity filter is not an activation gate in TRPV1-3 channels
Cited by: 34
Author(s): Andrés Jara-Oseguera, Katherine E. Huffer, Kenton J. Swartz
Software Mentions: 1
Published: almost 5 years ago

10.7554/eLife.20718

Assembling the Tat protein translocase
Cited by: 57
Author(s): Felicity Alcock, Phillip J. Stansfeld, Hajra Basit, Johann Habersetzer, Matthew A. B. Baker, Tracy Palmer, Mark I. Wallace, Ben C. Berks
Software Mentions: 1
Published: almost 8 years ago

10.7554/eLife.55571

Aromatic interactions with membrane modulate human BK channel activation
Cited by: 1
Author(s): Mahdieh Yazdani, Guohui Zhang, Zhiguang Jia, Jingyi Shi, Jianmin Cui, Jianhan Chen
Software Mentions: 1
Published: about 4 years ago

10.7554/eLife.58621

Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes
Cited by: 16
Author(s): Viviana Monje-Galvan, Gregory A. Voth
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms20051009

Exploring the Dual Interaction of Natural Rhamnolipids with Plant and Fungal Biomimetic Plasma Membranes through Biophysical Studies
Cited by: 38
Author(s): Noadya Monnier, Aurélien L. Furlan, Sébastien Buchoux, Magali Deleu, Manuel Dauchez, Sonia Rippa, Catherine Sarazin
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20174268

Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem
Cited by: 16
Author(s): Chetna Tyagi, Tamás Marik, Csaba Vágvölgyi, László Kredics, Ferenc Ötvös
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21093110

Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts
Cited by: 9
Author(s): Ivan Gushchin, Philipp Orekhov, I. A. Melnikov, Vitaly Polovinkin, Anastasia Yuzhakova, Valentin Gordeliy
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms21165933

How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs
Cited by: 29
Author(s): Mariona Torrens‐Fontanals, Tomasz Maciej Stępniewski, David Aranda-García, Adrián Morales-Pastor, Brian Medel-Lacruz, Jana Selent
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms22010445

Switching between Ultrafast Pathways Enables a Green-Red Emission Ratiometric Fluorescent-Protein-Based Ca2+ Biosensor
Cited by: 9
Author(s): Longteng Tang, Shuce Zhang, Y. B. Zhao, Nikita D. Rozanov, Lingbo Zhu, Jiahui Wu, Robert E. Campbell, Chong Fang
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22052548

Lipid Dynamics in Diisobutylene-Maleic Acid (DIBMA) Lipid Particles in Presence of Sensory Rhodopsin II
Cited by: 8
Author(s): Natalia Voskoboynikova, Philipp Orekhov, Marine E. Bozdaganyan, Felix Kodde, Malte Rademacher, Maurice Schowe, Annette Budke-Gieseking, Britta Brickwedde, Olympia E. Psathaki, Armen Y. Mulkidjanian, Katia Cosentino, К. В. Шайтан, Heinz−Jürgen Steinhoff
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms22158318

Comparative Molecular Dynamics Investigation of the Electromotile Hearing Protein Prestin
Cited by: 2
Author(s): Gianfranco Abrusci, Thomas Tarenzi, Mattia Sturlese, Gabriele Giachin, Roberto Battistutta, Gianluca Lattanzi
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms22168613

Membrane Association Modes of Natural Anticancer Peptides: Mechanistic Details on Helicity, Orientation, and Surface Coverage
Cited by: 8
Author(s): Mayra Quemé‐Peña, Tünde Juhász, Gergely Kohut, Maria Anastasia Ricci, Priyanka Singh, Imola Csilla Szigyártó, Ibolya Zita Papp, Lívia Fülöp, Tamás Beke‐Somfai
Software Mentions: 1
Published: about 3 years ago

10.3390/ijms22168999

Molecular Dynamics-Derived Pharmacophore Model Explaining the Nonselective Aspect of KV10.1 Pore Blockers
Cited by: 2
Author(s): Žan Toplak, Franci Merzel, Luis A. Pardo, Lucija Peterlin Mašič, Tihomir Tomašič
Software Mentions: 1
Published: about 3 years ago

10.1021/acscatal.1c01215

On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes
Cited by: 16
Author(s): Adam Pecina, Daniele Rosa‐Gastaldo, Laura Riccardi, Sebastian Franco-Ulloa, Emil Milan, Paolo Scrimin, Fabrizio Mancin, Marco De Vivo
Software Mentions: 1
Published: about 3 years ago

Projects: pypi: MDAnalysis

Papers Mentioning MDAnalysis 182