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: MDAnalysis
https://packages.ecosyste.ms/registries/pypi.org/packages/MDAnalysis
An object-oriented toolkit to analyze molecular dynamics trajectories.
48 versions
Latest release: about 1 year ago
21 dependent packages
22,261 downloads last month
Papers Mentioning MDAnalysis 182
10.1186/s12859-018-2367-z
Biotite: a unifying open source computational biology framework in PythonCited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: about 6 years ago
10.3390/biom11020338
Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional ConsiderationsCited by: 1
Author(s): Maroua Ben Amira, Mohamed Faize, Magnus Karlsson, Mukesh Dubey, Magdalena Frąc, Jacek Panek, Boris Fumanal, Aurélie Gousset-Dupont, Jean-Louis Julien, Hatem Chaar, Daniel Auguin, Robin Mom, Philippe Label, Jean-Stéphane Venisse
Software Mentions: 12
Published: over 3 years ago
10.1371/journal.pone.0256990
Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteinsCited by: 11
Author(s): Joe G Greener, David T. Jones
Software Mentions: 7
Published: about 3 years ago
10.1371/journal.pcbi.1008551
DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensemblesCited by: 39
Author(s): Giulio Tesei, João M. Martins, Micha B. A. Kunze, Yong Wang, Ramón Crehuet, Kresten Lindorff‐Larsen
Software Mentions: 7
Published: almost 4 years ago
10.7717/peerj.4013
PBxplore: a tool to analyze local protein structure and deformability with Protein BlocksCited by: 26
Author(s): Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G. de Brevern, Pierre Poulain
Software Mentions: 6
Published: almost 7 years ago
10.1186/s13321-021-00536-w
Learning protein-ligand binding affinity with atomic environment vectorsCited by: 21
Author(s): Rocco Meli, Andrew Anighoro, Michael J. Bodkin, Garrett M. Morris, Philip C. Biggin
Software Mentions: 6
Published: about 3 years ago
10.1016/j.csbj.2021.05.005
Comparison of the pH- and thermally-induced fluctuations of a therapeutic antibody Fab fragment by molecular dynamics simulationCited by: 6
Author(s): Cheng Zhang, Nuria Codina, Jiazhi Tang, Haoran Yu, Nesrine Chakroun, Frank Kozielski, Paul A. Dalby
Software Mentions: 6
Published: almost 4 years ago
10.1038/s41598-017-01498-6
An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of massCited by: 64
Author(s): Juan Salamanca Viloria, Maria Francesca Allega, Matteo Lambrughi, Elena Papaleo
Software Mentions: 6
Published: over 7 years ago
10.1016/j.str.2015.12.011
The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion EnvelopeCited by: 79
Author(s): Tyler Reddy, Mark S. P. Sansom
Software Mentions: 6
Published: over 8 years ago
10.3389/fcell.2020.601145
Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter SerotoninCited by: 11
Author(s): Anna Bochicchio, Astrid F. Brandner, Oskar Engberg, Daniel Huster, Rainer A. Böckmann
Software Mentions: 5
Published: almost 4 years ago
10.1021/acs.jcim.0c01179
Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force FieldsCited by: 13
Author(s): Riccardo Ocello, Simone Furini, Francesca Lugli, Maurizio Recanatini, Carmen Domene, Matteo Masetti
Software Mentions: 5
Published: almost 4 years ago
10.7554/eLife.58660
Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanismsCited by: 37
Author(s): Katherine E. Huffer, Antoniya A. Aleksandrova, Andrés Jara-Oseguera, Lucy R. Forrest, Kenton J. Swartz
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pcbi.1004568
Path Similarity Analysis: A Method for Quantifying Macromolecular PathwaysCited by: 43
Author(s): Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein
Software Mentions: 5
Published: about 9 years ago
10.1002/minf.202100031
ACE2‐Variants Indicate Potential SARS‐CoV‐2‐Susceptibility in Animals: A Molecular Dynamics StudyCited by: 7
Author(s): Szymon Pach, Trung Ngoc Nguyen, Jakob Trimpert, Dušan Kunec, Nikolaus Osterrieder, Gerhard Wolber
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pone.0231714
Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software applicationCited by: 0
Author(s): Kai Pua, Daisuke Yuhara, Sho Ayuba, Kenji Yasuoka
Software Mentions: 4
Published: over 4 years ago
10.3390/molecules25235505
Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJCited by: 5
Author(s): Sascha Jähnigen, Daniel Sebastiani
Software Mentions: 4
Published: almost 4 years ago
10.7717/peerj.266
Analyzing machupo virus-receptor binding by molecular dynamics simulationsCited by: 9
Author(s): Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, Claus O. Wilke
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pcbi.1008936
Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?Cited by: 15
Author(s): Jon Kapla, Ismael Rodríguez‐Espigares, Flavio Ballante, Jana Selent, Jens Carlsson
Software Mentions: 4
Published: over 3 years ago
10.1038/s42003-019-0748-0
Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulationsCited by: 35
Author(s): C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S. Parkinson, Phillip J. Stansfeld, Zaida Luthey‐Schulten, P. Zhang
Software Mentions: 4
Published: almost 5 years ago
10.1186/s13321-020-00451-6
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorialCited by: 9
Author(s): Simon Bray, Tharindu Senapathi, Christopher B. Barnett, Björn Grüning
Software Mentions: 4
Published: about 4 years ago
10.1126/sciadv.abh2217
Identification and assessment of cardiolipin interactions with <i>E. coli</i> inner membrane proteinsCited by: 33
Author(s): Robin A. Corey, Wanling Song, Anna L. Duncan, T. Bertie Ansell, Mark S. P. Sansom, Phillip J. Stansfeld
Software Mentions: 4
Published: about 3 years ago
10.7554/eLife.68380
A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrievalCited by: 10
Author(s): Andreas Gerondopoulos, Philipp Bräuer, Tomoaki Sobajima, Zhiyi Wu, Joanne L. Parker, Philip C. Biggin, Francis A. Barr, Simon Newstead
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-017-16865-6
Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranesCited by: 67
Author(s): Anna L. Duncan, Tyler Reddy, Heidi Koldsø, Jean Hélie, Philip W. Fowler, Matthieu Chavent, Mark S. P. Sansom
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pone.0167524
IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion ChannelsCited by: 1
Author(s): Kota Kasahara, Kengo Kinoshita
Software Mentions: 3
Published: almost 8 years ago
10.1038/s42003-018-0063-1
Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitopeCited by: 6
Author(s): Bankala Krishnarjuna, Toshihiko Sugiki, Rodrigo Morales, Jeffrey Seow, Toshimichi Fujiwara, Karyn L. Wilde, Raymond S. Norton, Christopher A. MacRaild
Software Mentions: 3
Published: over 6 years ago
10.3389/fmolb.2021.676976
From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of BiomoleculesCited by: 26
Author(s): Marco Giulini, Marta Rigoli, Giovanni Mattiotti, Roberto Menichetti, Thomas Tarenzi, Raffaele Fiorentini, Raffaello Potestio
Software Mentions: 3
Published: over 3 years ago
10.3390/biom11040529
Interaction of Ligands for PET with the Dopamine D3 Receptor: In Silico and In Vitro MethodsCited by: 6
Author(s): Chia-Ju Hsieh, Aladdin Riad, Ji Youn Lee, Kristoffer Sahlholm, Kuiying Xu, Robert R. Luedtke, Robert H. Mach
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-020-64088-z
Rational identification and characterisation of peptide ligands for targeting polysialic acidCited by: 1
Author(s): Divya G. Shastry, Flaviyan Jerome Irudayanathan, Arthur Robin Williams, Mattheos Koffas, Robert J. Linhardt, Shikha Nangia, Pankaj Karande
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1009772
Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodiesCited by: 68
Author(s): Marta Alenquer, Filipe Ferreira, Diana Lousa, Mariana Valério, Mónica Medina-Lopes, Marie‐Louise Bergman, Juliana Gonçalves, Jocelyne Demengeot, Ricardo B. Leite, Jingtao Lilue, Zemin Ning, Carlos Penha‐Gonçalves, Helena Soares, Cláudio M. Soares, Maria João Amorim
Software Mentions: 3
Published: over 3 years ago
10.3389/fmolb.2021.726232
3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics TrajectoriesCited by: 6
Author(s): Genís Bayarri, Modesto Orozco
Software Mentions: 3
Published: about 3 years ago
10.1016/j.csbj.2018.10.008
Quantitative comparison of ABC membrane protein type I exporter structures in a standardized wayCited by: 4
Author(s): Georgina Csizmadia, Bianka Farkas, Zoltán Spagina, Hedvig Tordai, Tamás Hegedüs
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pcbi.1007680
Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticityCited by: 31
Author(s): Mariama Jaiteh, Ismael Rodríguez‐Espigares, Jana Selent, Jens Carlsson
Software Mentions: 3
Published: over 4 years ago
10.3389/fphar.2017.00393
Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding PocketCited by: 6
Author(s): Tamir Dingjan, Anne Imberty, Serge Pérez, Elizabeth Yuriev, Paul A. Ramsland
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pcbi.1007856
State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membraneCited by: 10
Author(s): Marc A. Dämgen, Philip C. Biggin
Software Mentions: 3
Published: over 3 years ago
10.3389/fphy.2017.00010
MutSα's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine LearningCited by: 8
Author(s): Ryan L. Melvin, W. G. Thompson, Ryan Godwin, William H. Gmeiner, Freddie R. Salsbury
Software Mentions: 3
Published: over 7 years ago
10.1074/jbc.M115.671586
Structure and Function of the Escherichia coli Tol-Pal Stator Protein TolRCited by: 30
Author(s): Justyna Aleksandra Wojdyla, Erin E. Cutts, Renata Kaminska, Grigorios Papadakos, Jonathan T. S. Hopper, Phillip J. Stansfeld, David Staunton, Carol V. Robinson, Colin Kleanthous
Software Mentions: 3
Published: about 9 years ago
10.3389/fcell.2020.00350
Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane DomainsCited by: 26
Author(s): Juanjuan Su, Siewert J. Marrink, Manuel N. Melo
Software Mentions: 3
Published: over 4 years ago
10.1016/j.bpj.2016.06.028
Modeling Functional Motions of Biological Systems by Customized Natural MovesCited by: 6
Author(s): Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Péter Mináry
Software Mentions: 3
Published: over 8 years ago
10.1002/1878-0261.12502
Smyd2 conformational changes in response to p53 binding: role of the C‐terminal domainCited by: 9
Author(s): Balasubramanian Chandramouli, Gerry Melino, Giovanni Chillemi
Software Mentions: 3
Published: over 5 years ago
10.7554/eLife.08419
CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signalingCited by: 93
Author(s): C. Keith Cassidy, Benjamin A. Himes, Frances Joan D. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten, Peijun Zhang
Software Mentions: 3
Published: almost 9 years ago
10.3390/ijms21114146
Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New OpportunitiesCited by: 32
Author(s): Rodrigo Aguayo‐Ortiz, L. Michel Espinoza-Fonseca
Software Mentions: 2
Published: over 4 years ago
10.1038/s42003-021-01847-2
Water orientation and dynamics in the closed and open influenza B virus M2 proton channelsCited by: 15
Author(s): Martin D. Gelenter, Venkata S. Mandala, Michiel J.M. Niesen, Dina A. Sharon, Aurelio J. Dregni, Adam P. Willard, Mei Hong
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms21197261
Atomistic Structure and Dynamics of the Ca2+-ATPase Bound to Phosphorylated PhospholambanCited by: 6
Author(s): Rodrigo Aguayo‐Ortiz, L. Michel Espinoza-Fonseca
Software Mentions: 2
Published: about 4 years ago
10.3390/ijms21249588
Towards Performant Design of Carbon-Based Nanomotors for Hydrogen Separation through Molecular Dynamics SimulationsCited by: 1
Author(s): Sebastian Muraru, Mariana Ioniţă
Software Mentions: 2
Published: almost 4 years ago
10.3390/biom11070935
The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase ComplexCited by: 4
Author(s): Urszula Orzeł, Jakub Jakowiecki, Krzysztof Młynarczyk, Sławomir Filipek
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22020718
Rounding Out the Understanding of ACD Toxicity with the Discovery of Cyclic Forms of Actin OligomersCited by: 6
Author(s): Harper Smith, Nick Pinkerton, David B. Heisler, Elena Kudryashova, Aaron R Hall, Kelly R. Karch, Andrew Norris, Vicki H. Wysocki, Marcos Sotomayor, Emil Reisler, Dimitrios Vavylonis, Dmitri S. Kudryashov
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijms22105408
KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein StabilityCited by: 5
Author(s): Carter J. Wilson, Megan Chang, Mikko Karttunen, Wing‐Yiu Choy
Software Mentions: 2
Published: over 3 years ago
10.1016/j.csbj.2021.05.002
Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domainCited by: 33
Author(s): Zachariah P Schuurs, Edward Hammond, Stefano Elli, Timothy R. Rudd, Courtney J. Mycroft-West, Marcelo A. Lima, Mark A. Skidmore, Richard Karlsson, Yen-Hsi Chen, Ieva Bagdonaite, Zifeng Yang, Yassir A. Ahmed, Derek J. Richard, Jeremy E. Turnbull, Vito Ferro, Deirdre R. Coombe, Neha S. Gandhi
Software Mentions: 2
Published: almost 4 years ago
10.1021/acs.jpcb.1c01946
Implementation of the Freely Jointed Chain Model to Assess Kinetics and Thermodynamics of Thermosensitive Coil–Globule Transition by Markov StatesCited by: 4
Author(s): Patrick K. Quoika, Monica L. Fernández‐Quintero, Maren Podewitz, Florian Hofer, Klaus R. Liedl
Software Mentions: 2
Published: over 3 years ago
10.1113/JP277079
ORAI1 channel gating and selectivity is differentially altered by natural mutations in the first or third transmembrane domainCited by: 36
Author(s): Monica Bulla, Gergely Gyimesi, Jihee Kim, Rajesh Bhardwaj, Matthias A. Hediger, Maud Frieden, Nicolas Demaurex
Software Mentions: 2
Published: almost 6 years ago
10.1016/j.csbj.2020.09.017
The autoinhibited state of MKK4: Phosphorylation, putative dimerization and R134W mutant studied by molecular dynamics simulationsCited by: 8
Author(s): Ekaterina Shevchenko, Antti Poso, Tatu Pantsar
Software Mentions: 2
Published: almost 5 years ago
10.15252/embj.2020105908
Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9Cited by: 27
Author(s): Iven Winkelmann, Ryota Matsuoka, Pascal Meier, Denis Shutin, Chen‐Ou Zhang, Laura Orellana, Ricky Sexton, Michael Landreh, Carol V. Robinson, Oliver Beckstein, David Drew
Software Mentions: 2
Published: about 4 years ago
10.15252/embr.201847182
Multiple C2 domains and transmembrane region proteins ( <scp>MCTP</scp> s) tether membranes at plasmodesmataCited by: 78
Author(s): Marie Brault, J.P. Petit, Françoise Immel, William J Nicolas, Marie Glavier, Lysiane Brocard, Amèlia Gaston, Mathieu Fouché, Timothy J. Hawkins, Jean-Marc Crowet, Magali Grison, V. Germain, Marion Rocher, Max Kraner, Vikram Alva, Stéphane Claverol, Andrea Paterlini, Yrjö Helariutta, Magali Deleu, Laurence Lins, Jens Tilsner, Emmanuelle Bayer
Software Mentions: 2
Published: over 5 years ago
10.1039/c8fd00013a
Water and hydrophobic gates in ion channels and nanoporesCited by: 45
Author(s): Shanlin Rao, Charlotte I. Lynch, Gianni Klesse, Georgia E. Oakley, Phillip J. Stansfeld, Stephen J. Tucker, Mark S. P. Sansom
Software Mentions: 2
Published: almost 7 years ago
10.1039/c3fd00131h
NRas slows the rate at which a model lipid bilayer phase separatesCited by: 17
Author(s): Elizabeth Jefferys, Mark S.P. Sansom, Philip W. Fowler
Software Mentions: 2
Published: almost 11 years ago
10.3389/fcell.2020.00575
Simulations of Asymmetric Membranes Illustrate Cooperative Leaflet Coupling and Lipid AdaptabilityCited by: 23
Author(s): Madison Blumer, Sophia Harris, Mengzhe Li, Luis Martínez, Michael Untereiner, Peter N. Saeta, Timothy S. Carpenter, Helgi I. Ingólfsson, William F. Bennett
Software Mentions: 2
Published: over 4 years ago
10.3389/fcimb.2016.00160
Structural Insights into Substrate Recognition by Clostridium difficile SortaseCited by: 4
Author(s): Jui-Chieh Yin, Chun-Hsien Fei, Yen-Chen Lo, Y.-Y. Hsiao, Jyun-Cyuan Chang, Jay C. Nix, Yuan-Yu Chang, Lee‐Wei Yang, I-Hsiu Huang, Shuying Wang
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pcbi.1007922
All-atom simulation of the HET-s prion replicationCited by: 8
Author(s): Luca Terruzzi, Giovanni Spagnolli, Alberto Boldrini, Jesús R. Requena, Emiliano Biasini, Pietro Faccioli
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pcbi.1004381
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and MilestoningCited by: 58
Author(s): Lane Votapka, Rommie E. Amaro
Software Mentions: 2
Published: about 9 years ago
10.3389/fmolb.2020.586544
Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With CalmodulinCited by: 0
Author(s): Irène Pitard, Damien Monet, Pierre L. Goossens, Arnaud Blondel, Thérèse E. Malliavin
Software Mentions: 2
Published: almost 4 years ago
10.3389/fmolb.2021.644720
A Single Mutation in the Outer Lipid-Facing Helix of a Pentameric Ligand-Gated Ion Channel Affects Channel Function Through a Radially-Propagating MechanismCited by: 3
Author(s): Alessandro Crnjar, Susanne M. Mesoy, Sarah C. R. Lummis, Carla Molteni
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1007554
Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domainCited by: 10
Author(s): Vikas Dubey, Behruz Bozorg, Daniel Wüstner, Himanshu Khandelia
Software Mentions: 2
Published: about 4 years ago
10.3389/fphar.2018.00834
QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding LoopCited by: 9
Author(s): Alexander Zlobin, Yuliana A. Mokrushina, Stanislav S. Terekhov, Arthur O. Zalevsky, Т. В. Бобик, A. V. Stepanova, Maria Aliseychik, Olga V. Kartseva, С. В. Пантелеев, Andrey V. Golovin, Alexey A. Belogurov, Alexander G. Gabibov, Иван Смирнов
Software Mentions: 2
Published: over 6 years ago
10.1016/j.jbc.2021.100307
Structural basis of trehalose recognition by the mycobacterial LpqY-SugABC transporterCited by: 9
Author(s): Christopher M. Furze, Ignacio Delso, Enriqueta Casal, Collette S. Guy, Chloe Seddon, Chelsea M. Brown, Hadyn L. Parker, Anjana Radhakrishnan, Raúl Pacheco-Gómez, Phillip J. Stansfeld, Jesús Angulo, Alexander D. Cameron, Elizabeth Fullam
Software Mentions: 2
Published: almost 4 years ago
10.1007/s10858-021-00365-x
A COVID moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopyCited by: 9
Author(s): A.L. Kantsadi, Emma Cattermole, Minos‐Timotheos Matsoukas, Georgios A. Spyroulias, Ioannis Vakonakis
Software Mentions: 2
Published: over 3 years ago
10.1021/acs.jctc.0c01281
Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange PropertiesCited by: 29
Author(s): Kara K. Grotz, Sergio Cruz-León, Nadine Schwierz
Software Mentions: 2
Published: over 3 years ago
10.1186/s12915-017-0438-7
An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hookCited by: 7
Author(s): Clive S. Barker, Irina V. Meshcheryakova, Alla S. Kostyukova, Peter L. Freddolino, Fadel A. Samatey
Software Mentions: 2
Published: about 7 years ago
10.1186/1758-2946-6-4
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharingCited by: 13
Author(s): Julien Thibault, Daniel R. Roe, Julio C. Facelli, Thomas E. Cheatham
Software Mentions: 2
Published: almost 11 years ago
10.1186/s13321-017-0237-8
Scoria: a Python module for manipulating 3D molecular dataCited by: 6
Author(s): Patrick J. Ropp, Aaron J. Friedman, Jacob D. Durrant
Software Mentions: 2
Published: about 7 years ago
10.1186/s13321-021-00548-6
ProLIF: a library to encode molecular interactions as fingerprintsCited by: 61
Author(s): Cédric Bouysset, Sébastien Fiorucci
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.ppat.1006552
Structural analysis of P. falciparum KAHRP and PfEMP1 complexes with host erythrocyte spectrin suggests a model for cytoadherent knob protrusionsCited by: 27
Author(s): Erin E. Cutts, Niklas Laasch, Dirk M. Reiter, Raphael Trenker, Leanne M. Slater, Phillip J. Stansfeld, Ioannis Vakonakis
Software Mentions: 2
Published: about 7 years ago
10.1186/s13104-021-05536-5
libxtc: an efficient library for reading XTC-compressed MD trajectory dataCited by: 9
Author(s): Н. А. Крылов, Roman G. Efremov
Software Mentions: 2
Published: over 3 years ago
10.1073/pnas.1918387117
Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channelsCited by: 78
Author(s): Anna L. Duncan, Robin A. Corey, Mark S. P. Sansom
Software Mentions: 2
Published: over 4 years ago
10.1016/j.molcel.2020.06.013
Structure of the Inhibited State of the Sec TransloconCited by: 42
Author(s): S. Gerard, Belinda S. Hall, A. Zaki, Katherine Corfield, Peter Mayerhofer, Catia Costa, Daniel K. Whelligan, Philip C. Biggin, Rachel E. Simmonds, M.K. Higgins
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pcbi.1004415
ENCORE: Software for Quantitative Ensemble ComparisonCited by: 62
Author(s): Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff‐Larsen
Software Mentions: 2
Published: about 9 years ago
10.1002/prot.26036
Lysine–arginine advanced glycation end‐product cross‐links and the effect on collagen structure: A molecular dynamics studyCited by: 7
Author(s): Anthony Nash, Sang Noh, Helen L. Birch, Nora H. de Leeuw
Software Mentions: 2
Published: almost 4 years ago
10.1016/j.molcel.2019.06.037
Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P2 SynthesisCited by: 47
Author(s): Taki Nishimura, Michael Gecht, Roberto Covino, Gerhard Hummer, Michał A. Surma, Christian Klose, Hiroyuki Arai, Nozomu Kono, Christopher J. Stefan
Software Mentions: 2
Published: about 5 years ago
10.1126/sciadv.1500723
Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenanceCited by: 103
Author(s): Oleg Fedorov, Josefina Castex, C. Tallant, Dafydd R. Owen, Sarah Martin, Matteo Aldeghi, Octovia Monteiro, P. Filippakopoulos, S. Picaud, John D. Trzupek, Brian S. Gerstenberger, C. Bountra, Dominica Willmann, Christopher Wells, Martin Philpott, Catherine Rogers, Philip C. Biggin, P.E. Brennan, Mark E. Bunnage, Roland Schüle, Thomas Günther, Stefan Knapp, Susanne Müller
Software Mentions: 2
Published: almost 9 years ago
10.1371/journal.pone.0156963
Dynamics of Crowded Vesicles: Local and Global Responses to Membrane CompositionCited by: 28
Author(s): Daniel A. Holdbrook, Roland G. Huber, Thomas J. Piggot, Peter J. Bond, Syma Khalid
Software Mentions: 2
Published: over 8 years ago
10.1126/sciadv.abc1726
The prefusion structure of herpes simplex virus glycoprotein BCited by: 41
Author(s): Benjamin Vollmer, Vojtěch Pražák, Daven Vasishtan, Elizabeth Jefferys, A. Hernandez-Duran, Melina Vallbracht, Barbara G. Klupp, Thomas C. Mettenleiter, Marija Backović, F.A. Rey, Maya Topf, Kay Grünewald
Software Mentions: 2
Published: about 4 years ago
10.3390/molecules26082148
Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu PeptideCited by: 2
Author(s): Irtaza Hassan, Federica Ferraro, Petra Imhof
Software Mentions: 2
Published: over 3 years ago
10.1186/s12859-018-2507-5
Deep clustering of protein folding simulationsCited by: 64
Author(s): Debsindhu Bhowmik, Shang Gao, M. Todd Young, Arvind Ramanathan
Software Mentions: 2
Published: almost 6 years ago
10.3390/molecules26071877
In Silico Design and Selection of New Tetrahydroisoquinoline-Based CD44 Antagonist CandidatesCited by: 4
Author(s): Angel J. Ruiz-Moreno, Atilio Reyes Romero, Alexander Dömling, Marco A. Velasco-Velázquez
Software Mentions: 2
Published: over 3 years ago
10.3762/bjoc.16.206
Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody bindingCited by: 2
Author(s): Christopher B. Barnett, Tharindu Senapathi, Kevin J. Naidoo
Software Mentions: 2
Published: about 4 years ago
10.1038/s41598-017-06446-y
A novel proton transfer mechanism in the SLC11 family of divalent metal ion transportersCited by: 27
Author(s): Jonai Pujol‐Giménez, Matthias A. Hediger, Gergely Gyimesi
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-17243-y
The orientation and stability of the GPCR-Arrestin complex in a lipid bilayerCited by: 10
Author(s): Dali Wang, Hua-Zhong Yu, Xiangdong Liu, Jianqiang Liu, Chen Song
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-018-20227-1
Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulationsCited by: 23
Author(s): Jonathan Shearer, Syma Khalid
Software Mentions: 2
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10.1038/s41598-018-21357-2
Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to functionCited by: 23
Author(s): Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess
Software Mentions: 2
Published: over 6 years ago
10.1021/acsnano.1c00155
Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide NanotubesCited by: 11
Author(s): Martín Calvelo, Charlotte I. Lynch, Juan R. Granja, Mark S. P. Sansom, Rebeca García‐Fandiño
Software Mentions: 2
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10.1038/s41598-020-62460-7
The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old ReceptorCited by: 7
Author(s): François Inizan, Myriam Hanna, Maxim Stolyarchuk, Isaure Chauvot de Beauchêne, Luba Tchertanov
Software Mentions: 2
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10.1038/s41598-021-89556-y
ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importerCited by: 1
Author(s): Bárbara Abreu, Carlos Cruz, A. Sofia F. Oliveira, Cláudio M. Soares
Software Mentions: 2
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10.1038/s41598-021-94707-2
Conformational dynamics of androgen receptors bound to agonists and antagonistsCited by: 8
Author(s): Hyo Jin Gim, Jiyong Park, Michael E. Jung, K. N. Houk
Software Mentions: 2
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10.1038/s41598-021-96217-7
A multiscale approach for bridging the gap between potency, efficacy, and safety of small molecules directed at membrane proteinsCited by: 7
Author(s): Rodrigo Aguayo‐Ortiz, Jeffery Creech, Eric N. Jiménez-Vázquez, Guadalupe Guerrero-Serna, Nulang Wang, A.M. Rocha, Todd J. Herron, L. Michel Espinoza-Fonseca
Software Mentions: 2
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10.1038/s41598-021-96370-z
Tandem domain structure determination based on a systematic enumeration of conformationsCited by: 2
Author(s): Thérèse E. Malliavin
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0071380
Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics SimulationsCited by: 28
Author(s): Hong Zhu, Shiyan Xiao, Haojun Liang
Software Mentions: 2
Published: about 11 years ago
10.1016/j.str.2016.10.005
Functional Annotation of Ion Channel Structures by Molecular SimulationCited by: 60
Author(s): Jemma L. Trick, Sivapalan Chelvaniththilan, Gianni Klesse, Prafulla Aryal, E. Jayne Wallace, Stephen J. Tucker, Mark S. P. Sansom
Software Mentions: 2
Published: almost 8 years ago
10.1016/j.str.2019.10.019
A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics SimulationsCited by: 33
Author(s): Marc A. Dämgen, Philip C. Biggin
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.str.2020.01.012
Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics SimulationsCited by: 13
Author(s): Shanlin Rao, George T. Bates, Callum R. Matthews, Thomas D. Newport, Owen N. Vickery, Phillip J. Stansfeld
Software Mentions: 2
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10.1128/mBio.00452-21
Cryo-EM Structures of CusA Reveal a Mechanism of Metal-Ion ExportCited by: 15
Author(s): Mitchell A. Moseng, Meinan Lyu, Tanadet Pipatpolkai, Przemysław Glaza, Corey C. Emerson, Phoebe L. Stewart, Phillip J. Stansfeld, Edward Yu
Software Mentions: 2
Published: over 3 years ago
10.1007/s00232-020-00152-z
Phosphatidylglyerol Lipid Binding at the Active Site of an Intramembrane ProteaseCited by: 6
Author(s): Ana‐Nicoleta Bondar
Software Mentions: 2
Published: almost 4 years ago