Ana Sofia F Oliveira (A Sofia Oliveira, Sofia Oliveira, A Sofia F Oliveira, Ana Sofia Oliveira, A S F Oliveira, A Sofia F Oliveira)

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 36

Top Topics

Mycobacterium Tuberculosis

Protein Protein

Arabidopsis Thaliana

Molecular Dynamics

Top Venues

Journal of the American Chemical Society

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Aunlika Chimprasit, Patchreenart Saparpakorn, Supa Hannongbua, James Spencer, Ana Sofia F Oliveira, Adrian J Mulholland, Pornpan Pungpo
Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations. Biochemistry 63 (11) (2024)
Benjamin J Hardy, Paulina Dubiel, Ethan L Bungay, May Rudin, Christopher Williams, Christopher J Arthur, Matthew J Guberman-Pfeffer, Ana Sofia F Oliveira, Paul Curnow, John Leslie Ross Anderson
Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design. Protein science : a publication of the Protein Society 33 (8) (2024)
Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Aunlika Chimprasit, Patchreenart Saparpakorn, Supa Hannongbua, James Spencer, Ana Sofia F Oliveira, Adrian J Mulholland, Pornpan Pungpo
Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations. Biochemistry (2024)
Benjamin J Hardy, Paulina Dubiel, Ethan L Bungay, May Rudin, Christopher Williams, Christopher J Arthur, Matthew J Guberman-Pfeffer, Ana Sofia F Oliveira, Paul Curnow, John Leslie Ross Anderson
Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design. Protein science : a publication of the Protein Society 33 (8) (2024)
Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Aunlika Chimprasit, Patchreenart Saparpakorn, Supa Hannongbua, James Spencer, Ana Sofia F Oliveira, Adrian J Mulholland, Pornpan Pungpo
Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations. Biochemistry 63 (11) (2024)
Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Aunlika Chimprasit, Patchreenart Saparpakorn, Supa Hannongbua, James Spencer, Ana Sofia F Oliveira, Adrian J Mulholland, Pornpan Pungpo
Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations. Biochemistry 63 (11) (2024)
Ana Sofia F Oliveira, J Rubio, C E M Noble, John Leslie Ross Anderson, J Anders, Adrian J Mulholland
Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (1) (2023)
Matteo Castelli, Filippo Marchetti, Sílvia Osuna, Ana Sofia F Oliveira, Adrian J Mulholland, Stefano Artin Serapian, Giorgio Colombo
Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society 146 (1) (2023)
George H Hutchins, Claire E M Noble, H Adrian Bunzel, Christopher Williams, Paulina Dubiel, Sathish K N Yadav, Paul M Molinaro, Rob Barringer, Hector Blackburn, Benjamin J Hardy, Alice E Parnell, Charles Landau, Paul R Race, Thomas A A Oliver, Ronald L Koder, Matthew P Crump, Christiane Schaffitzel, Ana Sofia F Oliveira, Adrian J Mulholland, John Leslie Ross Anderson
An expandable, modular de novo protein platform for precision redox engineering. Proceedings of the National Academy of Sciences of the United States of America 120 (31) (2023)
H T Henry Chan, Ana Sofia F Oliveira, Christopher J Schofield, Adrian J Mulholland, Fernanda Duarte
Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease. JACS Au 3 (6) (2023)
Ana Sofia F Oliveira, J Rubio, C E M Noble, John Leslie Ross Anderson, J Anders, Adrian J Mulholland
Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (1) (2023)
Matteo Castelli, Filippo Marchetti, Sílvia Osuna, Ana Sofia F Oliveira, Adrian J Mulholland, Stefano Artin Serapian, Giorgio Colombo
Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society 146 (1) (2023)
Ana Sofia F Oliveira, J Rubio, C E M Noble, John Leslie Ross Anderson, J Anders, Adrian J Mulholland
Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations. Journal of chemical theory and computation (2023)
Matteo Castelli, Filippo Marchetti, Sílvia Osuna, Ana Sofia F Oliveira, Adrian J Mulholland, Stefano Artin Serapian, Giorgio Colombo
Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society 146 (1) (2023)
Ana Sofia F Oliveira, J Rubio, C E M Noble, John Leslie Ross Anderson, J Anders, Adrian J Mulholland
Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (1) (2023)
Matteo Castelli, Filippo Marchetti, Sílvia Osuna, Ana Sofia F Oliveira, Adrian J Mulholland, Stefano Artin Serapian, Giorgio Colombo
Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society (2023)
Matteo Castelli, Filippo Marchetti, Sílvia Osuna, Ana Sofia F Oliveira, Adrian J Mulholland, Stefano Artin Serapian, Giorgio Colombo
Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society 146 (1) (2023)
H T Henry Chan, Ana Sofia F Oliveira, Christopher J Schofield, Adrian J Mulholland, Fernanda Duarte
Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease. JACS Au 3 (6) (2023)
Leonor Guerra-Guimarães, Carla Pinheiro, Ana Sofia F Oliveira, Andrea Mira-Jover, Javier Valverde, Fernanda Alves de Freitas Guedes, Herlander Azevedo, Vitor Várzea, Antonio Jesús Muñoz Pajares
Publisher Correction: The chloroplast protein HCF164 is predicted to be associated with Coffea S H 9 resistance factor against Hemileia vastatrix. Scientific reports 13 (1) (2023)
H T Henry Chan, Ana Sofia F Oliveira, Christopher J Schofield, Adrian J Mulholland, Fernanda Duarte
Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease. JACS Au 3 (6) (2023)
Ana Sofia F Oliveira, Deborah K Shoemark, Andrew D Davidson, Imre Berger, Christiane Schaffitzel, Adrian J Mulholland
SARS-CoV-2 spike variants differ in their allosteric response to linoleic acid. Journal of molecular cell biology (2023)
Matteo Castelli, Filippo Marchetti, Sílvia Osuna, Ana Sofia F Oliveira, Adrian J Mulholland, Stefano Artin Serapian, Giorgio Colombo
Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society 146 (1) (2023)
H T Henry Chan, Ana Sofia F Oliveira, Christopher J Schofield, Adrian J Mulholland, Fernanda Duarte
Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease. JACS Au 3 (6) (2023)
Leonor Guerra-Guimarães, Carla Pinheiro, Ana Sofia F Oliveira, Andrea Mira-Jover, Javier Valverde, Fernanda Alves de Freitas Guedes, Herlander Azevedo, Vitor Várzea, Antonio Jesús Muñoz Pajares
The chloroplast protein HCF164 is predicted to be associated with Coffea S H 9 resistance factor against Hemileia vastatrix. Scientific reports 13 (1) (2023)
Deborah E Daniels, Ivan Ferrer-Vicens, Joseph Hawksworth, Tatyana N Andrienko, Elizabeth M Finnie, Natalie S Bretherton, Daniel C J Ferguson, Ana Sofia F Oliveira, Jenn-Yeu A Szeto, Marieangela C Wilson, John N Brewin, Jan Frayne
Human cellular model systems of β-thalassemia enable in-depth analysis of disease phenotype. Nature communications 14 (1) (2023)
Ana Sofia F Oliveira, J Rubio, C E M Noble, John Leslie Ross Anderson, J Anders, Adrian J Mulholland
Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations. Journal of chemical theory and computation 20 (1) (2023)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
William John Allen, Robin Adam Corey, Daniel W Watkins, Ana Sofia F Oliveira, Kiel Hards, Gregory M Cook, Ian Collinson
Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion. eLife 11 (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Juan Facundo Chrestia, Ana Sofia F Oliveira, Adrian J Mulholland, Timothy Gallagher, Isabel Bermudez, Cecilia Bouzat
A Functional Interaction Between Y674-R685 Region of the SARS-CoV-2 Spike Protein and the Human α7 Nicotinic Receptor. Molecular neurobiology 59 (10) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Samia A Elseginy, Ana Sofia F Oliveira, Deborah K Shoemark, Richard B Sessions
Identification and validation of novel microtubule suppressors with an imidazopyridine scaffold through structure-based virtual screening and docking. RSC medicinal chemistry 13 (8) (2022)
Kapil Gupta, Christine Toelzer, Maia Kavanagh Williamson, Deborah K Shoemark, Ana Sofia F Oliveira, David A Matthews, Abdulaziz Almuqrin, Oskar Staufer, Sathish K N Yadav, Ufuk Borucu, Frederic Garzoni, Daniel Fitzgerald, Joachim Pius Spatz, Adrian J Mulholland, Andrew D Davidson, Christiane Schaffitzel, Imre Berger
Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2. Nature communications 13 (1) (2022)
Ana Sofia F Oliveira, Giovanni Ciccotti, Shozeb Haider, Adrian J Mulholland
Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems. The European physical journal. B 94 (7) (2021)
Teresa Mínguez-Viñas, Beatriz Elizabeth Nielsen, Deborah K Shoemark, Cecilia Gotti, Richard B Sessions, Adrian J Mulholland, Cecilia Bouzat, Susan Wonnacott, Timothy Gallagher, Isabel Bermudez, Ana Sofia F Oliveira
A conserved arginine with non-conserved function is a key determinant of agonist selectivity in α7 nicotinic ACh receptors. British journal of pharmacology 178 (7) (2021)