pypi: MDAnalysis | Projects | Ecosyste.ms: Papers

10.1186/s12859-018-2367-z

Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: about 6 years ago

Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations
Cited 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: almost 4 years ago

10.1371/journal.pone.0256990

Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins
Cited by: 11
Author(s): Joe G Greener, David T. Jones
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1008551

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
Cited 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 Blocks
Cited 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: about 7 years ago

10.1186/s13321-021-00536-w

Learning protein-ligand binding affinity with atomic environment vectors
Cited by: 21
Author(s): Rocco Meli, Andrew Anighoro, Michael J. Bodkin, Garrett M. Morris, Philip C. Biggin
Software Mentions: 6
Published: over 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 simulation
Cited 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 mass
Cited 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 Envelope
Cited by: 79
Author(s): Tyler Reddy, Mark S. P. Sansom
Software Mentions: 6
Published: almost 9 years ago

10.3389/fcell.2020.601145

Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin
Cited by: 11
Author(s): Anna Bochicchio, Astrid F. Brandner, Oskar Engberg, Daniel Huster, Rainer A. Böckmann
Software Mentions: 5
Published: about 4 years ago

10.1021/acs.jcim.0c01179

Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields
Cited by: 13
Author(s): Riccardo Ocello, Simone Furini, Francesca Lugli, Maurizio Recanatini, Carmen Domene, Matteo Masetti
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.58660

Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms
Cited by: 37
Author(s): Katherine E. Huffer, Antoniya A. Aleksandrova, Andrés Jara-Oseguera, Lucy R. Forrest, Kenton J. Swartz
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1004568

Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
Cited 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 Study
Cited by: 7
Author(s): Szymon Pach, Trung Ngoc Nguyen, Jakob Trimpert, Dušan Kunec, Nikolaus Osterrieder, Gerhard Wolber
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0231714

Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application
Cited 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 AnPixJ
Cited by: 5
Author(s): Sascha Jähnigen, Daniel Sebastiani
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.266

Analyzing machupo virus-receptor binding by molecular dynamics simulations
Cited by: 9
Author(s): Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, Claus O. Wilke
Software Mentions: 4
Published: almost 11 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 simulations
Cited 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 tutorial
Cited by: 9
Author(s): Simon Bray, Tharindu Senapathi, Christopher B. Barnett, Björn Grüning
Software Mentions: 4
Published: over 4 years ago

10.1126/sciadv.abh2217

Identification and assessment of cardiolipin interactions with <i>E. coli</i> inner membrane proteins
Cited 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: over 3 years ago

10.7554/eLife.68380

A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval
Cited 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 membranes
Cited 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: about 7 years ago

10.1371/journal.pone.0167524

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels
Cited by: 1
Author(s): Kota Kasahara, Kengo Kinoshita
Software Mentions: 3
Published: about 8 years ago

10.1038/s42003-018-0063-1

Transient antibody-antigen interactions mediate the strain-specific recognition of a conserved malaria epitope
Cited 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 Biomolecules
Cited 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 Methods
Cited 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 acid
Cited 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 antibodies
Cited 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 Trajectories
Cited by: 6
Author(s): Genís Bayarri, Modesto Orozco
Software Mentions: 3
Published: over 3 years ago

10.1016/j.csbj.2018.10.008

Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way
Cited 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 plasticity
Cited by: 31
Author(s): Mariama Jaiteh, Ismael Rodríguez‐Espigares, Jana Selent, Jens Carlsson
Software Mentions: 3
Published: almost 5 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 Pocket
Cited 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 membrane
Cited by: 10
Author(s): Marc A. Dämgen, Philip C. Biggin
Software Mentions: 3
Published: almost 4 years ago

10.3389/fphy.2017.00010

MutSα's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning
Cited 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 TolR
Cited 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 Domains
Cited 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 Moves
Cited 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 domain
Cited 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 signaling
Cited 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: about 9 years ago

10.3390/ijms21114146

Linking Biochemical and Structural States of SERCA: Achievements, Challenges, and New Opportunities
Cited 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 channels
Cited 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: almost 4 years ago

10.3390/ijms21197261

Atomistic Structure and Dynamics of the Ca2+-ATPase Bound to Phosphorylated Phospholamban
Cited 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 Simulations
Cited by: 1
Author(s): Sebastian Muraru, Mariana Ioniţă
Software Mentions: 2
Published: about 4 years ago

10.3390/biom11070935

The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex
Cited 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 Oligomers
Cited 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 Stability
Cited 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 domain
Cited 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 States
Cited 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 domain
Cited by: 36
Author(s): Monica Bulla, Gergely Gyimesi, Jihee Kim, Rajesh Bhardwaj, Matthias A. Hediger, Maud Frieden, Nicolas Demaurex
Software Mentions: 2
Published: about 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 simulations
Cited 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 NHE9
Cited 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 plasmodesmata
Cited 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 nanopores
Cited 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 separates
Cited 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 Adaptability
Cited 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 Sortase
Cited 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: about 8 years ago

10.1371/journal.pcbi.1007922

All-atom simulation of the HET-s prion replication
Cited by: 8
Author(s): Luca Terruzzi, Giovanni Spagnolli, Alberto Boldrini, Jesús R. Requena, Emiliano Biasini, Pietro Faccioli
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1004381

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Cited 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 Calmodulin
Cited by: 0
Author(s): Irène Pitard, Damien Monet, Pierre L. Goossens, Arnaud Blondel, Thérèse E. Malliavin
Software Mentions: 2
Published: about 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 Mechanism
Cited 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 domain
Cited 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 Loop
Cited 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 transporter
Cited 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 spectroscopy
Cited 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 Properties
Cited by: 29
Author(s): Kara K. Grotz, Sergio Cruz-León, Nadine Schwierz
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12915-017-0438-7

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook
Cited 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 sharing
Cited 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 data
Cited by: 6
Author(s): Patrick J. Ropp, Aaron J. Friedman, Jacob D. Durrant
Software Mentions: 2
Published: over 7 years ago

10.1186/s13321-021-00548-6

ProLIF: a library to encode molecular interactions as fingerprints
Cited 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 protrusions
Cited 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: over 7 years ago

10.1186/s13104-021-05536-5

libxtc: an efficient library for reading XTC-compressed MD trajectory data
Cited 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) channels
Cited 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 Translocon
Cited 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 Comparison
Cited 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 study
Cited 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 Synthesis
Cited 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: over 5 years ago

10.1126/sciadv.1500723

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance
Cited 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: about 9 years ago

10.1371/journal.pone.0156963

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition
Cited 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 B
Cited 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 Peptide
Cited 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 simulations
Cited by: 64
Author(s): Debsindhu Bhowmik, Shang Gao, M. Todd Young, Arvind Ramanathan
Software Mentions: 2
Published: about 6 years ago

10.3390/molecules26071877

In Silico Design and Selection of New Tetrahydroisoquinoline-Based CD44 Antagonist Candidates
Cited 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 binding
Cited 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 transporters
Cited 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 bilayer
Cited by: 10
Author(s): Dali Wang, Hua-Zhong Yu, Xiangdong Liu, Jianqiang Liu, Chen Song
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-20227-1

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations
Cited by: 23
Author(s): Jonathan Shearer, Syma Khalid
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-21357-2

Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
Cited by: 23
Author(s): Viveca Lindahl, Pontus Gourdon, Magnus Andersson, Berk Hess
Software Mentions: 2
Published: almost 7 years ago

10.1021/acsnano.1c00155

Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes
Cited by: 11
Author(s): Martín Calvelo, Charlotte I. Lynch, Juan R. Granja, Mark S. P. Sansom, Rebeca García‐Fandiño
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-62460-7

The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor
Cited by: 7
Author(s): François Inizan, Myriam Hanna, Maxim Stolyarchuk, Isaure Chauvot de Beauchêne, Luba Tchertanov
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-89556-y

ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer
Cited by: 1
Author(s): Bárbara Abreu, Carlos Cruz, A. Sofia F. Oliveira, Cláudio M. Soares
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-94707-2

Conformational dynamics of androgen receptors bound to agonists and antagonists
Cited by: 8
Author(s): Hyo Jin Gim, Jiyong Park, Michael E. Jung, K. N. Houk
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-96217-7

A multiscale approach for bridging the gap between potency, efficacy, and safety of small molecules directed at membrane proteins
Cited 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
Published: over 3 years ago

10.1038/s41598-021-96370-z

Tandem domain structure determination based on a systematic enumeration of conformations
Cited by: 2
Author(s): Thérèse E. Malliavin
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0071380

Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations
Cited by: 28
Author(s): Hong Zhu, Shiyan Xiao, Haojun Liang
Software Mentions: 2
Published: over 11 years ago

10.1016/j.str.2016.10.005

Functional Annotation of Ion Channel Structures by Molecular Simulation
Cited 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: about 8 years ago

10.1016/j.str.2019.10.019

A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations
Cited 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 Simulations
Cited by: 13
Author(s): Shanlin Rao, George T. Bates, Callum R. Matthews, Thomas D. Newport, Owen N. Vickery, Phillip J. Stansfeld
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.00452-21

Cryo-EM Structures of CusA Reveal a Mechanism of Metal-Ion Export
Cited 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 Protease
Cited by: 6
Author(s): Ana‐Nicoleta Bondar
Software Mentions: 2
Published: about 4 years ago

Projects: pypi: MDAnalysis

Papers Mentioning MDAnalysis 182