Ecosyste.ms: Papers

10.3389/fmicb.2021.720991

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases
Cited by: 5
Author(s): Edgar Olehnovics, Junqi Yin, Adrià Pérez, Gianni De Fabritiis, Robert A. Bonomo, Debsindhu Bhowmik, Shozeb Haider
Software Mentions: 5
Published: about 3 years ago

10.1098/rsfs.2020.0007

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
Cited by: 71
Author(s): Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
Software Mentions: 5
Published: about 4 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

10.3389/fmolb.2021.720561

Exploring Ligand Binding to Calcitonin Gene-Related Peptide Receptors
Cited by: 5
Author(s): Giuseppe Deganutti, Silvia Atanasio, Roxana Maria Rujan, Patrick M. Sexton, Denise Wootten, Christopher A. Reynolds
Software Mentions: 4
Published: about 3 years ago

10.1074/jbc.M116.770271

Nanostructure and stability of calcitonin amyloids
Cited by: 14
Author(s): Federica Rigoldi, Pierangelo Metrangolo, Alberto Redaelli, Alfonso Gautieri
Software Mentions: 3
Published: over 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: over 4 years ago

10.1186/s12915-021-01102-4

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding
Cited by: 9
Author(s): Hüseyin İlgü, Jean-Marc Jeckelmann, David Kalbermatter, Zöhre Ucurum, Thomas Lemmin, Dimitrios Fotiadis
Software Mentions: 3
Published: about 3 years ago

10.3389/fchem.2020.00107

Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?
Cited by: 14
Author(s): Maicol Bissaro, Mattia Sturlese, Stefano Moro
Software Mentions: 3
Published: over 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

10.1038/s41598-018-19991-x

Thermal stabilization of the deglycating enzyme Amadoriase I by rational design
Cited by: 18
Author(s): Federica Rigoldi, Stefano Donini, Francesca Giacomina, Federico Sorana, Alberto Redaelli, Tiziano Bandiera, Emilio Parisini, Alfonso Gautieri
Software Mentions: 3
Published: over 6 years ago

10.1002/jcc.24030

Best bang for your buck: GPU nodes for <scp>GROMACS</scp> biomolecular simulations
Cited by: 180
Author(s): Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-018-19345-7

Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs
Cited by: 39
Author(s): Noelia Ferruz, Stefan Doerr, Michelle Vanase-Frawley, Yang Zou, Xiaomin Chen, Eric S. Marr, Robin T. Nelson, Bethany L. Kormos, Travis T. Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola, Gianni De Fabritiis
Software Mentions: 3
Published: almost 7 years ago

10.1007/s00253-019-09760-9

Interaction of carbohydrate-binding modules with poly(ethylene terephthalate)
Cited by: 33
Author(s): Jeannette Weber, Dušan Petrović, Birgit Strodel, Sander H. J. Smits, Stephan Kolkenbrock, Christian Leggewie, Karl‐Erich Jaeger
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.M117.779496

Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R)
Cited by: 43
Author(s): Cassandra Koole, Christopher A. Reynolds, Juan Carlos Mobarec, Caroline A. Hick, Patrick M. Sexton, Thomas P. Sakmar
Software Mentions: 2
Published: over 7 years ago

10.1016/j.jmb.2016.09.021

MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca 2+ Ion Bound at the Constriction Zone
Cited by: 28
Author(s): Luana Ferrara, Gregor D. Wallat, L. Moynié, Naresh Niranjan Dhanasekar, Soumeya Aliouane, Silvia Acosta‐Gutiérrez, Jean‐Marie Pagès, Jean‐Michel Bolla, Mathias Winterhalter, Matteo Ceccarelli, James H. Naismith
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.11050

Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel
Cited by: 31
Author(s): Chloé Habermacher, Adeline Martz, Nicolas Calimet, Damien Lemoine, Laurie Peverini, Alexandre Specht, Marco Cecchini, Thomas Grütter
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.66567

Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics
Cited by: 35
Author(s): Ioannis Galdadas, Shen Qu, A. Sofia F. Oliveira, Edgar Olehnovics, Andrew R Mack, María F Mojica, Pratul K. Agarwal, C.L. Tooke, Francesco Luigi Gervasio, James Spencer, Robert A. Bonomo, Adrian J. Mulholland, Shozeb Haider
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0179936

Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome
Cited by: 34
Author(s): Zheng Zhao, Lei Xie, Philip E. Bourne
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms20071686

Distinct Dopamine D2 Receptor Antagonists Differentially Impact D2 Receptor Oligomerization
Cited by: 24
Author(s): Elise Wouters, Adrián Ricarte Marín, James A. R. Dalton, Jesús Giraldo
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms20164041

Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach
Cited by: 13
Author(s): Deborah Palazzotti, Maicol Bissaro, Giovanni Bolcato, Andrea Astolfi, Tommaso Felicetti, Stefano Sabatini, Mattia Sturlese, Violetta Cecchetti, Maria Letizia Barreca, Stefano Moro
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1007818

Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions
Cited by: 18
Author(s): Agustín Bruzzese, James A. R. Dalton, Jesús Giraldo
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-22735-6

Structural insights into positive and negative allosteric regulation of a G protein-coupled receptor through protein-lipid interactions
Cited by: 34
Author(s): Agustín Bruzzese, Carles Gil, James A. R. Dalton, Jesús Giraldo
Software Mentions: 2
Published: over 6 years ago

10.1080/14756366.2021.1954919

Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332
Cited by: 55
Author(s): Matteo Pavan, Giovanni Bolcato, Davide Bassani, Mattia Sturlese, Stefano Moro
Software Mentions: 2
Published: almost 4 years ago

10.3390/molecules24152752

Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A2A Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations
Cited by: 7
Author(s): Maicol Bissaro, Giovanni Bolcato, Giuseppe Deganutti, Mattia Sturlese, Stefano Moro
Software Mentions: 2
Published: over 5 years ago

10.3390/molecules25204623

In Silico Molecular Study of Tryptophan Bitterness
Cited by: 8
Author(s): Antonella Di Pizio, Alessandro Nicoli
Software Mentions: 2
Published: about 4 years ago

10.1016/j.ejpb.2019.02.007

Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning
Cited by: 63
Author(s): Shakhawath Hossain, Aleksei Kabedev, Albin Parrow, Christel A S Bergström, Per Larsson
Software Mentions: 2
Published: over 5 years ago

10.1038/srep33776

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter
Cited by: 1
Author(s): Li-Ying Wang, Vidhya Ravi, Gérard Leblanc, Esteve Padrós, Josep Cladera, Àlex Perálvarez-Marín
Software Mentions: 2
Published: about 8 years ago

10.3390/molecules23051134

Carbazole Derivatives’ Binding to c-KIT G-Quadruplex DNA
Cited by: 21
Author(s): Agata Głuszyńska, Bernard Juskowiak, Martyna Kuta-Siejkowska, Marcin Hoffmann, Shozeb Haider
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-017-11370-2

Development of Fluorescent Probes that Target Serotonin 5-HT2B Receptors
Cited by: 15
Author(s): Jhonny Azuaje, Paula Cadaveira López, Alejandro Villamor Iglesias, Rocío Ailim de la Fuente, José M. Pérez-Rubio, Davinia Moreno, Tomasz Maciej Stępniewski, Xerardo García‐Mera, José Brea, Jana Selent, Dolores Péréz, Marián Castro, Marı́a Isabel Loza, Eddy Sotelo
Software Mentions: 2
Published: about 7 years ago

10.1016/j.bcp.2016.12.013

High affinity binding of the peptide agonist TIP-39 to the parathyroid hormone 2 (PTH 2 ) receptor requires the hydroxyl group of Tyr-318 on transmembrane helix 5
Cited by: 7
Author(s): Richard E. Weaver, Juan Carlos Mobarec, Mark Wigglesworth, Christopher A. Reynolds, Daniel P. Donnelly
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-16842-z

An engineered opsin monomer scrambles phospholipids
Cited by: 12
Author(s): Kalpana Pandey, Birgit Ploier, Michael A. Goren, Joshua Levitz, George Khelashvili, Anant K. Menon
Software Mentions: 2
Published: almost 7 years ago

10.1080/14756366.2020.1838499

HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR
Cited by: 9
Author(s): Francesca Ferrari, Maicol Bissaro, Simone Fabbian, Jessica de Almeida Roger, Stefano Mammi, Stefano Moro, Massimo Bellanda, Mattia Sturlese
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-016-0941-9

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology
Cited by: 43
Author(s): Zheng Zhao, Che L. Martin, Raymond Fan, Philip E. Bourne, Lei Xie
Software Mentions: 2
Published: over 8 years ago

10.1126/sciadv.abb8368

Distinct phosphorylation sites in a prototypical GPCR differently orchestrate β-arrestin interaction, trafficking, and signaling
Cited by: 50
Author(s): Hemlata Dwivedi-Agnihotri, Madhu Chaturvedi, Mithu Baidya, Tomasz Maciej Stępniewski, Shubhi Pandey, Jagannath Maharana, Ashish Srivastava, Natarin Caengprasath, Aylin Hanyaloglu, Jana Selent, Arun K. Shukla
Software Mentions: 1
Published: about 4 years ago

10.1038/srep19839

Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors
Cited by: 86
Author(s): Ramón Guixà-González, Matti Javanainen, Maricel Gómez-Soler, Begoña Cordobilla, Joan Carles Domingo, Ferrán Sanz, Manuel Pastor, Francisco Ciruela, Hector Martinez‐Seara, Jana Selent
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep30275

Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme
Cited by: 16
Author(s): Noelia Ferruz, Gary Tresadern, Antonio Pineda–Lucena, Gianni De Fabritiis
Software Mentions: 1
Published: over 8 years ago

10.1038/srep40076

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter
Cited by: 59
Author(s): Asghar M. Razavi, George Khelashvili, Harel Weinstein
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-02037-z

Angiotensin II type 1/adenosine A 2A receptor oligomers: a novel target for tardive dyskinesia
Cited by: 12
Author(s): Paulo Alexandre de Oliveira, James A. R. Dalton, Marc López-Cano, Adrián Ricarte, Xavier Morató, Filipe C. Matheus, Andréia S. Cunha, Christa E. Müller, Reinaldo Ν. Takahashi, Víctor Fernández-Dueñas, Jesús Giraldo, Rui Daniel Prediger, Francisco Ciruela
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-05095-5

Analysis of positive and negative allosteric modulation in metabotropic glutamate receptors 4 and 5 with a dual ligand
Cited by: 11
Author(s): James A. R. Dalton, Jean‐Philippe Pin, Jesús Giraldo
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-11483-8

Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity
Cited by: 43
Author(s): Anoop Kapoor, Gerard Martínez-Rosell, Davide Provasi, Gianni De Fabritiis, Marta Filizola
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-31176-0

Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance
Cited by: 25
Author(s): Ioannis Galdadas, Silvia Lovera, Guillermo Pérez‐Hernández, Melissa D. Barnes, Jess Healy, Hamidreza Afsharikho, Neil Woodford, Robert A. Bonomo, Francesco Luigi Gervasio, Shozeb Haider
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-50752-6

Reconstruction of apo A2A receptor activation pathways reveal ligand-competent intermediates and state-dependent cholesterol hotspots
Cited by: 23
Author(s): Silvia Lovera, Alberto Cuzzolin, Sebastian Kelm, Gianni De Fabritiis, Zara A. Sands
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-53078-5

Understanding allosteric interactions in hMLKL protein that modulate necroptosis and its inhibition
Cited by: 15
Author(s): Nupur Bansal, Simone Sciabola, Govinda Bhisetti
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-59120-1

The endocannabinoid hydrolase FAAH is an allosteric enzyme
Cited by: 22
Author(s): Enrico Dainese, Sergio Oddi, Monica Simonetti, Annalaura Sabatucci, Clotilde B. Angelucci, Alice Ballone, Beatrice Dufrusine, Filomena Fezza, Gianni De Fabritiis, Mauro Maccarrone
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-69322-2

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations
Cited by: 12
Author(s): Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Software Mentions: 1
Published: over 4 years ago

10.1128/mBio.02085-18

Deciphering the Evolution of Cephalosporin Resistance to Ceftolozane-Tazobactam in Pseudomonas aeruginosa
Cited by: 55
Author(s): Melissa D. Barnes, Magdalena A. Taracila, Joseph Rutter, Christopher R. Bethel, Ioannis Galdadas, Andrea M. Hujer, Emilia Caselli, Fabio Prati, John P. Dekker, Krisztina M. Papp-Wallace, Shozeb Haider, Robert A. Bonomo
Software Mentions: 1
Published: almost 6 years ago

10.7554/eLife.33038

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies
Cited by: 62
Author(s): Victor Ovchinnikov, Joy E Louveau, John P. Barton, Martin Karplus, Arup K. Chakraborty
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.53444

Exchange of water for sterol underlies sterol egress from a StARkin domain
Cited by: 16
Author(s): George Khelashvili, Neha Chauhan, Kalpana Pandey, David Eliezer, Anant K. Menon
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms20184641

The Anti-Amyloidogenic Action of Doxycycline: A Molecular Dynamics Study on the Interaction with Aβ42
Cited by: 28
Author(s): Alfonso Gautieri, Marten Beeg, Marco Gobbi, Federica Rigoldi, Laura Colombo, Mario Salmona
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22084078

Dopamine D2 Receptor Agonist Binding Kinetics—Role of a Conserved Serine Residue
Cited by: 5
Author(s): Richard Ågren, Tomasz Maciej Stępniewski, Hugo Zeberg, Jana Selent, Kristoffer Sahlholm
Software Mentions: 1
Published: over 3 years ago

10.3390/antibiotics10060635

The Influence of Permeability through Bacterial Porins in Whole-Cell Compound Accumulation
Cited by: 9
Author(s): Silvia Acosta‐Gutiérrez, Igor Bodrenko, Matteo Ceccarelli
Software Mentions: 1
Published: over 3 years ago

10.1186/s13023-016-0416-0

GNAO1 encephalopathy: further delineation of a severe neurodevelopmental syndrome affecting females
Cited by: 34
Author(s): Anna Marcé‐Grau, James A. R. Dalton, J. López Pisón, M.C. García-Jiménez, L. Monge Galindo, Ester Cuenca-León, Jesús Giraldo, Alfons Macaya
Software Mentions: 1
Published: over 8 years ago

10.1186/s12915-018-0495-6

How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties
Cited by: 34
Author(s): Asghar M. Razavi, George Khelashvili, Harel Weinstein
Software Mentions: 1
Published: over 6 years ago

10.1016/j.bcp.2016.08.015

Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor
Cited by: 41
Author(s): Denise Wootten, Christopher A. Reynolds, Kevin J. Smith, Juan Carlos Mobarec, Sebastian G.B. Furness, Laurence J. Miller, Arthur Christopoulos, Patrick M. Sexton
Software Mentions: 1
Published: about 8 years ago

10.1016/j.bcp.2017.07.005

Receptor activity-modifying protein dependent and independent activation mechanisms in the coupling of calcitonin gene-related peptide and adrenomedullin receptors to Gs
Cited by: 30
Author(s): Michael J. Woolley, Christopher A. Reynolds, John Simms, Christopher S. Walker, Juan Carlos Mobarec, Michael L. Garelja, Alex C. Conner, David R. Poyner, Debbie L. Hay
Software Mentions: 1
Published: about 7 years ago

10.3390/biom10050686

Computational Investigations on the Binding Mode of Ligands for the Cannabinoid-Activated G Protein-Coupled Receptor GPR18
Cited by: 12
Author(s): Alexander Neumann, Viktor Engel, Andhika B. Mahardhika, Clara T. Schoeder, Vigneshwaran Namasivayam, Katarzyna Kieć‐Kononowicz, Christian Müller
Software Mentions: 1
Published: over 4 years ago

10.1111/bph.14960

Cell‐permeable high‐affinity tracers for G _q proteins provide structural insights, reveal distinct binding kinetics and identify small molecule inhibitors
Cited by: 19
Author(s): Markus Kuschak, Vigneshwaran Namasivayam, Muhammad Rafehi, Jan H. Voß, Jaspal Garg, Jonathan G. Schlegel, Aliaa Abdelrahman, Stefan Kehraus, Raphael Reher, Jim Küppers, Katharina Sylvester, Sonja Hinz, Michaela Matthey, Daniela Wenzel, Bernd K. Fleischmann, Alexander Pfeifer, Asuka Inoue, Michael Gütschow, Gabriele M. König, Christa E. Müller
Software Mentions: 1
Published: over 4 years ago

10.3390/brainsci8040063

Mechanistic Insights into the Stimulant Properties of Novel Psychoactive Substances (NPS) and Their Discrimination by the Dopamine Transporter—In Silico and In Vitro Exploration of Dissociative Diarylethylamines
Cited by: 15
Author(s): Michelle A. Sahai, Charles S. Davidson, Neelakshi Dutta, Jolanta Opacka‐Juffry
Software Mentions: 1
Published: over 6 years ago

10.3390/molecules26040973

Electron Paramagnetic Resonance Gives Evidence for the Presence of Type 1 Gonadotropin-Releasing Hormone Receptor (GnRH-R) in Subdomains of Lipid Rafts
Cited by: 1
Author(s): Tilen Koklič, Alenka Hrovat, Ramón Guixà-González, Ismael Rodríguez‐Espigares, Damaris Navio, Robert Frangež, Matjaž Uršič, Valentina Kubale, Ana Plemenitaš, Jana Selent, Marjeta Šentjurc, Milka Vrecl
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules25235747

Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria
Cited by: 9
Author(s): Alessandro Pira, Mariano Andrea Scorciapino, Igor Bodrenko, Andrea Bosin, Silvia Acosta‐Gutiérrez, Matteo Ceccarelli
Software Mentions: 1
Published: almost 4 years ago

10.3390/molecules25204651

Comparing Fragment Binding Poses Prediction Using HSP90 as a Key Study: When Bound Water Makes the Difference
Cited by: 4
Author(s): Giovanni Bolcato, Maicol Bissaro, Mattia Sturlese, Stefano Moro
Software Mentions: 1
Published: about 4 years ago

10.3390/pharmaceutics13081266

An Iron Shield to Protect Epigallocatehin-3-Gallate from Degradation: Multifunctional Self-Assembled Iron Oxide Nanocarrier Enhances Protein Kinase CK2 Intracellular Targeting and Inhibition
Cited by: 3
Author(s): Luca Fasolato, Massimiliano Magro, Giorgio Cozza, Ferruccio Sbarra, Simone Molinari, Enrico Novelli, Fábio Vianello, Andrea Venerando
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pcbi.1000884

Induced Effects of Sodium Ions on Dopaminergic G-Protein Coupled Receptors
Cited by: 97
Author(s): Jana Selent, Ferrán Sanz, Manuel Pastor, Gianni De Fabritiis
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pcbi.1004578

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics
Cited by: 57
Author(s): Silvia Lovera, Maria Morando, Encarna Pucheta-Martínez, Jorge L. Martı́nez-Torrecuadrada, Giorgio Saladino, Francesco Luigi Gervasio
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0193479

The importance of negative determinants as modulators of CK2 targeting. The lesson of Akt2 S131
Cited by: 1
Author(s): J Vilardell, Cristina Girardi, Oriano Marin, Giorgio Cozza, Lorenzo A. Pinna, Maria Ruzzene
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0042023

Membrane-Sensitive Conformational States of Helix 8 in the Metabotropic Glu2 Receptor, a Class C GPCR
Cited by: 30
Author(s): Agostino Bruno, Gabriele Costantino, Gianni De Fabritiis, Manuel Pastor, Jana Selent
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0121378

ALK Kinase Domain Mutations in Primary Anaplastic Large Cell Lymphoma: Consequences on NPM-ALK Activity and Sensitivity to Tyrosine Kinase Inhibitors
Cited by: 7
Author(s): Federica Lovisa, Giorgio Cozza, Andrea Cristiani, Alberto Cuzzolin, Alessandro Albiero, Lara Mussolin, Marta Pillon, Stefano Moro, Giuseppe Basso, Angelo Rosolen, Paolo Bonvini
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0109312

A Dynamic View of Molecular Switch Behavior at Serotonin Receptors: Implications for Functional Selectivity
Cited by: 26
Author(s): Maria Martí-Solano, Ferrán Sanz, Manuel Pastor, Jana Selent
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0103879

Charged Residues Distribution Modulates Selectivity of the Open State of Human Isoforms of the Voltage Dependent Anion-Selective Channel
Cited by: 46
Author(s): Giuseppe Amodeo, Mariano Andrea Scorciapino, Angela Messina, Vito De Pinto, Matteo Ceccarelli
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0129846

Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations
Cited by: 4
Author(s): Kai Wang, Shiyang Long, Pu Tian
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0019302

Mastering the Canonical Loop of Serine Protease Inhibitors: Enhancing Potency by Optimising the Internal Hydrogen Bond Network
Cited by: 60
Author(s): Joakim E. Swedberg, Simon J. de Veer, Kei Chun Sit, Cyril Reboul, Ashley M. Buckle, Jonathan M. Harris
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0250635

Observing spontaneous, accelerated substrate binding in molecular dynamics simulations of glutamate transporters
Cited by: 3
Author(s): Jiali Wang, Peifan Li, Xiaozhen Yu, Christof Grewer
Software Mentions: 1
Published: over 3 years ago

10.1039/d1sc00749a

Mechanistic insights into dopaminergic and serotonergic neurotransmission – concerted interactions with helices 5 and 6 drive the functional outcome
Cited by: 6
Author(s): Tomasz Maciej Stępniewski, Arturo Mancini, Richard Ågren, Mariona Torrens‐Fontanals, Meriem Semache, Michel Bouvier, Kristoffer Sahlholm, Billy Breton, Jana Selent
Software Mentions: 1
Published: almost 4 years ago

10.3389/fimmu.2019.02000

Magnesium Restores Activity to Peripheral Blood Cells in a Patient With Functionally Impaired Interleukin-2-Inducible T Cell Kinase
Cited by: 9
Author(s): Matthew K. Howe, Kennichi C. Dowdell, Amitava Roy, Julie E. Niemela, Wyndham H. Wilson, Joshua McElwee, Jason D. Hughes, Jeffrey I. Cohen
Software Mentions: 1
Published: about 5 years ago

10.3389/fnmol.2019.00207

Insights From Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders
Cited by: 15
Author(s): João Marcelo Lamim Ribeiro, Marta Filizola
Software Mentions: 1
Published: about 5 years ago

10.3389/fnmol.2017.00146

Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins
Cited by: 27
Author(s): Rachel T. Wragg, Daniel Parisotto, Zhenlong Li, Mayu S. Terakawa, David Snead, Ishani Basu, Harel Weinstein, David Eliezer, Jeremy S. Dittman
Software Mentions: 1
Published: over 7 years ago

10.3389/fphar.2020.00806

The Role of Dopamine in the Stimulant Characteristics of Novel Psychoactive Substances (NPS)—Neurobiological and Computational Assessment Using the Case of Desoxypipradrol (2-DPMP)
Cited by: 5
Author(s): Barbara Loi, Michelle A. Sahai, Maria Antonietta De Luca, Hana Shiref, Jolanta Opacka‐Juffry
Software Mentions: 1
Published: over 4 years ago

10.3389/fphar.2018.00923

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview
Cited by: 352
Author(s): Veronica Salmaso, Stefano Moro
Software Mentions: 1
Published: about 6 years ago

10.1074/jbc.M116.751362

Receptor Activity-modifying Protein-directed G Protein Signaling Specificity for the Calcitonin Gene-related Peptide Family of Receptors
Cited by: 70
Author(s): Cathryn Weston, Ian J. Winfield, Matthew Harris, Rose Hodgson, Archna Shah, Simon J. Dowell, Juan Carlos Mobarec, David A. Woodlock, Christopher A. Reynolds, David R. Poyner, Harriet A. Watkins, Graham Ladds
Software Mentions: 1
Published: about 8 years ago

10.1021/acs.jcim.0c00053

Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute
Cited by: 3
Author(s): Silvia Rinaldi, Giorgio Colombo, Antonella Paladino
Software Mentions: 1
Published: over 4 years ago

10.1021/acs.jctc.0c01343

TorchMD: A Deep Learning Framework for Molecular Simulations
Cited by: 85
Author(s): Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noé, Toni Giorgino, Gianni De Fabritiis
Software Mentions: 1
Published: over 3 years ago

10.1080/14756366.2017.1404592

Synthesis and preliminary structure-activity relationship study of 2-aryl-2<i>H</i>-pyrazolo[4,3-<i>c</i>]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors
Cited by: 5
Author(s): Ivana Malvacio, Alberto Cuzzolin, Mattia Sturlese, D. Mariano A. Vera, Elizabeth L. Moyano, Stefano Moro
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.ppat.1005821

Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence
Cited by: 40
Author(s): Rigard Mélanie, Jeanette E. Bröms, Anne Mosnier, Maggy Hologne, Amandine Martin, Lindgren Lena, Punginelli Claire, Claire Lays, Olivier Walker, Alain Charbit, Telouk Philippe, Wayne Conlan, Laurent Terradot, Anders Sjöstedt, Thomas Henry
Software Mentions: 1
Published: about 8 years ago

10.1016/j.redox.2021.102070

Production and purification of homogenous recombinant human selenoproteins reveals a unique codon skipping event in E. coli and GPX4-specific affinity to bromosulfophthalein
Cited by: 14
Author(s): Qing Cheng, Antonella Roveri, Giorgio Cozza, Luciana Bordin, Isabelle Rohn, Tanja Schwerdtle, Anna P. Kipp, Fulvio Ursini, Matilde Maiorino, Giovanni Miotto, Elias S.J. Arnér
Software Mentions: 1
Published: about 3 years ago