Rommie E. Amaro

Biochemistry, Genetics and Molecular BiologyComputer ScienceMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 86 papers. Top paper: “Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein”.

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

ACS Central Science(2020)10.1021/acscentsci.0c01056

N/A

10.3DataRank · unranked

1078 citations

Zied Gaieb, Jory A. Goldsmith, Christy K. Hjorth, Abigail C. Dommer, Aoife M. Harbison +7 more

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology

PLoS Computational Biology(2010)10.1371/journal.pcbi.1000648

N/A

2.7DataRank · unranked

76 citations

Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen +7 more

Distinct pathways for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses

PLoS Pathogens(2024)10.1371/journal.ppat.1012704

N/A

0.461DataRank · unranked

10 citations

Cory M. Acreman, Inna Ricardo-Lax, Jacob Berrigan, Gorka Lasso, Toheeb A. Balogun +12 more

Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanism

ACS Central Science(2020)10.1021/acscentsci.9b01071

N/A

0DataRank · unranked

117 citations

Sarah E. Kochanek, Lorenzo Casalino, Pek U. Ieong, Abigail C. Dommer, Rommie E. Amaro +1 more

Markov state models and NMR uncover an overlooked allosteric loop in p53

Chemical Science(2020)10.1039/d0sc05053a

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0DataRank · unranked

47 citations

Özlem Demir, Jenaro Soto, Melanie J. Cocco, Rommie E. Amaro, Emília P. Barros

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007756

N/A

0DataRank · unranked

75 citations

Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, J. Andrew McCammon, Ravi Ramamoorthi +3 more

Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase

Biophysical Journal(2020)10.1016/j.bpj.2020.10.024

N/A

0DataRank · unranked

21 citations

Lorenzo Casalino, Robert Konečný, Gary Huber, Rommie E. Amaro, J. Andrew McCammon +1 more

An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models

Frontiers in Molecular Biosciences(2020)10.3389/fmolb.2020.00093

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0DataRank · unranked

18 citations

Zied Gaieb, Rommie E. Amaro, conor parks

An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Biophysical Journal(2020)10.1016/j.bpj.2019.11.3400

N/A

0DataRank · unranked

37 citations

Justin G. Laughlin, J. B. Moody, Rommie E. Amaro, J. Andrew McCammon, Michael Holst +2 more

Biomolecular Simulations in the Time of COVID-19, and After

Computing in Science & Engineering(2020)10.1109/mcse.2020.3024155

N/A

0DataRank · unranked

31 citations

Adrian J. Mulholland, Rommie E. Amaro

SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.28.424451

N/A

0DataRank · unranked

281 citations

Giulia Piccini, Danilo Licastro, Lorenzo Casalino, Nicole V. Johnson, Ida Paciello +13 more

Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.11.146522

N/A

0DataRank · unranked

82 citations

Zied Gaieb, Jory A. Goldsmith, Christy K. Hjorth, Abigail C. Dommer, Aoife M. Harbison +7 more

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.19.390187

N/A

0DataRank · unranked

46 citations

Abigail C. Dommer, Zied Gaieb, Emília P. Barros, Terra Sztain, Surl-Hee Ahn +23 more

Elucidation of cryptic and allosteric pockets within the SARS-CoV-2 protease

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.23.218784

N/A

0DataRank · unranked

24 citations

Rommie E. Amaro, J. Andrew McCammon, Terra Sztain

Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.16.206680

N/A

0DataRank · unranked

20 citations

Amaurys Avila Ibarra, Isabel Bermudez, Lorenzo Casalino, Zied Gaieb, Deborah K. Shoemark +5 more

The flexibility of ACE2 in the context of SARS-CoV-2 infection

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.16.300459

N/A

0DataRank · unranked

19 citations

Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, Yanbin Wang, Lucy Fallon +5 more

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.02.323915

N/A

0DataRank · unranked

18 citations

Alexander J. Pak, Peng He, Viviana Monje‐Galvan, Lorenzo Casalino, Zied Gaieb +4 more

Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.08.12.248690

N/A

0DataRank · unranked

3 citations

Lorenzo Casalino, Robert Konečný, Gary Huber, Rommie E. Amaro, J. Andrew McCammon +1 more

Benchmarking ensemble docking methods as a scientific outreach project

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.02.324343

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0DataRank · unranked

1 citations

Dhruv Kumar, Cynthia Chen, Bryn C. Taylor, Benjamin R. Jagger, Rommie E. Amaro +2 more

Disease related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveals a path to selective inhibitors

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.01.406264

N/A

0DataRank · unranked

0 citations

Zied Gaieb, Kaelin D. Fleming, Chiara Borsari, Noah J Harris, Brandon E. Moeller +4 more

A glycan gate controls opening of the SARS-CoV-2 spike protein

Nature Chemistry(2021)10.1038/s41557-021-00758-3

N/A

0DataRank · unranked

411 citations

Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, E. Seitz +12 more

SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2103154118

N/A

0DataRank · unranked

378 citations

Giulia Piccini, Danilo Licastro, Lorenzo Casalino, Nicole V. Johnson, Ida Paciello +13 more

A critical overview of computational approaches employed for COVID-19 drug discovery

Chemical Society Reviews(2021)10.1039/d0cs01065k

N/A

0DataRank · unranked

212 citations

Rommie E. Amaro, Carolina Horta Andrade, Nathan Brown, Sean Ekins, Denis Fourches +14 more

A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors

Biophysical Journal(2021)10.1016/j.bpj.2021.01.037

N/A

0DataRank · unranked

79 citations

Amaurys Ávila Ibarra, Isabel Bermudez, Lorenzo Casalino, Zied Gaieb, Deborah K. Shoemark +5 more

Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease

Journal of Chemical Information and Modeling(2021)10.1021/acs.jcim.1c00140

N/A

0DataRank · unranked

74 citations

Rommie E. Amaro, J. Andrew McCammon, Terra Sztain

Disease-related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors

eLife(2021)10.7554/elife.64691

N/A

0DataRank · unranked

56 citations

Zied Gaieb, Kaelin D. Fleming, Chiara Borsari, Noah J Harris, Brandon E. Moeller +4 more

GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses

ACS Central Science(2021)10.1021/acscentsci.1c01080

N/A

0DataRank · unranked

52 citations

Fiona L. Kearns, Mia A. Rosenfeld, Lorenzo Casalino, Micah J. Papanikolas, Carlos Simmerling +3 more

Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates

Cell Reports(2021)10.1016/j.celrep.2021.109840

N/A

0DataRank · unranked

42 citations

Nicholas Wauer, Satarupa Bhaduri, Adam Conn, Saroj Gourkanti, Narinderbir Singh +5 more

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins

Nature Communications(2021)10.1038/s41467-020-18911-w

N/A

0DataRank · unranked

51 citations

Lindsey Doyle, Justin Daho Lee, Michael Rappleye, Lauren Gagnon, Min Yen Lee +14 more

Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00770

N/A

0DataRank · unranked

39 citations

Anupam Anand Ojha, Rommie E. Amaro, J. Andrew McCammon, Surl-Hee Ahn

Development of Dimethylisoxazole-Attached Imidazo[1,2-a]pyridines as Potent and Selective CBP/P300 Inhibitors

Journal of Medicinal Chemistry(2021)10.1021/acs.jmedchem.0c02232

N/A

0DataRank · unranked

31 citations

Virangika K. Wimalasena, Hailemichael O. Yosief, Melissa J. Bikowitz, Logan H. Sigua, Tingjian Wang +10 more

An integrated view of p53 dynamics, function, and reactivation

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2020.11.005

N/A

0DataRank · unranked

30 citations

Emília P. Barros, Tavina L. Offutt, Mia A. Rosenfeld, Rommie E. Amaro, Özlem Demir

Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2105230118

N/A

0DataRank · unranked

27 citations

Mauricio J. del Razo, Christopher T. Lee, Bryn C. Taylor, Rommie E. Amaro, Frank Noé +1 more

RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control

Biomolecules(2021)10.3390/biom11010076

N/A

0DataRank · unranked

17 citations

Özlem Demir, Panpan You, Antonio Sarno, Rommie E. Amaro, Hilde Nilsen +1 more

A glycan gate controls opening of the SARS-CoV-2 spike protein

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.02.15.431212

N/A

0DataRank · unranked

70 citations

Surl-Hee Ahn, Anthony T. Bogetti, Lorenzo Casalino, Jory A. Goldsmith, E. Seitz +12 more

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.11.12.468428

N/A

0DataRank · unranked

28 citations

Lorenzo Casalino, Fiona L. Kearns, Mia A. Rosenfeld, Nicholas Wauer, Surl-Hee Ahn +47 more

Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.02.438274

N/A

0DataRank · unranked

24 citations

Ke Shi, Özlem Demir, Surajit Banerjee, Lulu Yin, Christopher Belica +4 more

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

UCL Discovery (University College London)(2021)10.33774/chemrxiv-2021-rzq4n

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0DataRank · unranked

13 citations

Rima Al‐awar, Rommie E. Amaro, C.H. Arrowsmith, Hátylas Azevedo, Robert A. Batey +34 more

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamic and kinetic sampling

ChemRxiv(2021)10.26434/chemrxiv-2021-2j2zr-v2

N/A

0DataRank · unranked

4 citations

Anupam Anand Ojha, Rommie E. Amaro, J. Andrew McCammon, Surl-Hee Ahn

Independent Markov Decomposition: Towards modeling kinetics of biomolecular complexes

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.24.436806

N/A

0DataRank · unranked

3 citations

Mauricio J. del Razo, Christopher T. Lee, Bryn C. Taylor, Rommie E. Amaro, Frank Noé +1 more

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamic and kinetic sampling

Figshare(2021)10.33774/chemrxiv-2021-2j2zr-v2

N/A

0DataRank · unranked

3 citations

Anupam Anand Ojha, Rommie E. Amaro, J. Andrew McCammon, Surl-Hee Ahn

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamics and kinetics sampling

(2021)10.33774/chemrxiv-2021-2j2zr

N/A

0DataRank · unranked

1 citations

Anupam Anand Ojha, Rommie E. Amaro, J. Andrew McCammon, Surl-Hee Ahn

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamics and kinetics sampling

ChemRxiv(2021)10.26434/chemrxiv-2021-2j2zr

N/A

0DataRank · unranked

0 citations

Anupam Anand Ojha, Rommie E. Amaro, J. Andrew McCammon, Surl-Hee Ahn

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

ChemRxiv(2021)10.26434/chemrxiv-2021-rzq4n

N/A

0DataRank · unranked

0 citations

Rima Al‐awar, Rommie E. Amaro, C.H. Arrowsmith, Hátylas Azevedo, Robert A. Batey +34 more

Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2106379119

N/A

0DataRank · unranked

194 citations

Ke Shi, Özlem Demir, Christopher Belica, Surajit Banerjee, Lulu Yin +4 more

Architecture and self-assembly of the jumbo bacteriophage nuclear shell

Nature(2022)10.1038/s41586-022-05013-4

N/A

0DataRank · unranked

114 citations

Amar Deep, Amy Prichard, Christian Seitz, Yajie Gu, Eray Enüstün +10 more

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

The International Journal of High Performance Computing Applications(2022)10.1177/10943420221128233

N/A

0DataRank · unranked

98 citations

Lorenzo Casalino, Fiona L. Kearns, Mia A. Rosenfeld, Nicholas Wauer, Surl-Hee Ahn +47 more

Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities

ACS Central Science(2022)10.1021/acscentsci.2c00981

N/A

0DataRank · unranked

72 citations

Christian Seitz, Julia Lederhofer, Yaroslav Tsybovsky, Ian A. Wilson, Masaru Kanekiyo +2 more

Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection

Nature Chemical Biology(2022)10.1038/s41589-022-01149-6

N/A

0DataRank · unranked

35 citations

Tomohiro Nakamura, Nathan Beutler, Xu Zhang, Juan Piña-Crespo, Maria Talantova +24 more

Discovery of compounds that reactivate p53 mutants in vitro and in vivo

Cell chemical biology(2022)10.1016/j.chembiol.2022.07.003

N/A

0DataRank · unranked

30 citations

Özlem Demir, Bryant Lim, Roberta Baronio, Delia F. Tifrea, Linda Hall +17 more

Brownian dynamics simulations of biomolecular diffusional association processes

Wiley Interdisciplinary Reviews Computational Molecular Science(2022)10.1002/wcms.1649

N/A

0DataRank · unranked

24 citations

Lane Votapka, Rommie E. Amaro, Rebecca C. Wade, Abraham Muñiz‐Chicharro

Inhibition of PRMT5 by market drugs as a novel cancer therapeutic avenue

Genes & Diseases(2022)10.1016/j.gendis.2022.04.001

N/A

0DataRank · unranked

16 citations

Matthew Martin, Lan Chen, Özlem Demir, Jiamin Jin, Xiumei Huang +13 more

Benchmarking ensemble docking methods in D3R Grand Challenge 4

Journal of Computer-Aided Molecular Design(2022)10.1007/s10822-021-00433-2

N/A

0DataRank · unranked

8 citations

Dhruv Kumar, Cynthia Chen, Bryn C. Taylor, Benjamin R. Jagger, Rommie E. Amaro +2 more

Brownian dynamics simulations of biomolecular diffusional association processes

Zenodo (CERN European Organization for Nuclear Research)(2022)10.5281/zenodo.8388056

N/A

0DataRank · unranked

3 citations

Lane Votapka, Rommie E. Amaro, Rebecca C. Wade, Abraham Muñiz‐Chicharro

Architecture and self-assembly of the jumbo bacteriophage nuclear shell

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.14.480162

N/A

0DataRank · unranked

18 citations

Amar Deep, Amy Prichard, Christian Seitz, Yajie Gu, Eray Enüstün +10 more

Targeting N-Myc in Neuroblastoma with Selective Aurora Kinase A Degraders

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.09.487756

N/A

0DataRank · unranked

5 citations

Ramkumar Moorthy, Özlem Demir, Zachary D. Baker, Jordan A. Naumann, Katherine F. M. Jones +10 more

Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.08.02.502576

N/A

0DataRank · unranked

5 citations

Christian Seitz, Julia Lederhofer, Yaroslav Tsybovsky, Ian A. Wilson, Masaru Kanekiyo +2 more

DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced kinetic and thermodynamic sampling

ChemRxiv(2022)10.26434/chemrxiv-2022-k6dr2

N/A

0DataRank · unranked

2 citations

Saumya Thakur, Surl-Hee Ahn, Rommie E. Amaro, Anupam Anand Ojha

DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling

ChemRxiv(2022)10.26434/chemrxiv-2022-k6dr2-v2

N/A

0DataRank · unranked

2 citations

Saumya Thakur, Surl-Hee Ahn, Rommie E. Amaro, Anupam Anand Ojha

Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.10.516058

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0DataRank · unranked

2 citations

Ambuj Srivastava, Lane Votapka, Rommie E. Amaro, Anupam Anand Ojha

DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling

ChemRxiv(2022)10.26434/chemrxiv-2022-k6dr2-v3

N/A

0DataRank · unranked

1 citations

Saumya Thakur, Surl-Hee Ahn, Rommie E. Amaro, Anupam Anand Ojha

SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx

Cell Reports Physical Science(2023)10.1016/j.xcrp.2023.101346

N/A

0DataRank · unranked

59 citations

Fiona L. Kearns, Mia A. Rosenfeld, Lane Votapka, Lorenzo Casalino, Micah Papanikolas +3 more

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Nature Communications(2023)10.1038/s41467-023-41756-y

N/A

0DataRank · unranked

51 citations

Alexandra D. Steigmeyer, Keira E. Mahoney, Mia A. Rosenfeld, Taryn M. Lucas, Courtney M. Smith +15 more

Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.2c01589

N/A

0DataRank · unranked

25 citations

Ambuj Srivastava, Lane Votapka, Rommie E. Amaro, Anupam Anand Ojha

QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Chemical Science(2023)10.1039/d3sc04195f

N/A

0DataRank · unranked

15 citations

Lane Votapka, Rommie E. Amaro, Anupam Anand Ojha

Multiscale computational modeling of the effects of 2’-deoxy-ATP on cardiac muscle calcium handling

Journal of Applied Physics(2023)10.1063/5.0157935

N/A

0DataRank · unranked

5 citations

Abigail E. Teitgen, Kimberly J. McCabe, Sophia P. Hirakis, Gary Huber, Michael Regnier +4 more

APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization

ACS Medicinal Chemistry Letters(2023)10.1021/acsmedchemlett.2c00517

N/A

0DataRank · unranked

4 citations

Mohamed Shehata, Michael A. Carpenter, Rommie E. Amaro, Daniel A. Harki, Katherine F. M. Jones

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.01.526488

N/A

0DataRank · unranked

5 citations

Alexandra D. Steigmeyer, Keira E. Mahoney, Mia A. Rosenfeld, Taryn M. Lucas, Deniz Ince +12 more

An introductory tutorial to the SEEKR2 (Simulation enabled estimation of kinetic rates v. 2) multiscale milestoning software [Article v1.0]

ChemRxiv(2023)10.26434/chemrxiv-2023-kd1wt

N/A

0DataRank · unranked

1 citations

Lane Votapka, Gary Huber, Shang Gao, Rommie E. Amaro, Anupam Anand Ojha

Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c00613

N/A

0DataRank · unranked

23 citations

Mia A. Rosenfeld, Rommie E. Amaro, Fiona L. Kearns

NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c00899

N/A

0DataRank · unranked

3 citations

Lane Votapka, Marcus Hock, Abigail E. Teitgen, J. Andrew McCammon, Andrew D. McCulloch +2 more

An Introductory Tutorial to the SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v. 2) Multiscale Milestoning Software [Article v1.0]

Living Journal of Computational Molecular Science(2024)10.33011/livecoms.5.1.2359

N/A

0DataRank · unranked

2 citations

Lane Votapka, Gary Huber, Shang Gao, Rommie E. Amaro, Anupam Anand Ojha

A critical overview of computational approaches employed for COVID-19 drug discovery

UNC Libraries(2024)10.17615/bwe6-fp72

N/A

0DataRank · unranked

5 citations

Kenneth M. Merz, Matthew H. Todd, José L. Medina‐Franco, Sean Ekins, Alexey Zakharov +14 more

Electrophysical cardiac remodeling at the molecular level: Insights into ryanodine receptor activation and calcium-induced calcium release from a stochastic explicit-particle model

Biophysical Journal(2024)10.1016/j.bpj.2024.09.029

N/A

0DataRank · unranked

1 citations

Thomas M. Bartol, Ludovic Autin, Rommie E. Amaro, Terrence J. Sejnowski, Sophia P. Hirakis

Breaking Down the Bottlebrush: Atomically-Detailed Structural Dynamics of Mucins

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.09.588790

N/A

0DataRank · unranked

2 citations

Mia A. Rosenfeld, Rommie E. Amaro, Fiona L. Kearns

Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.25.591187

N/A

0DataRank · unranked

0 citations

Özlem Demir, Mackenzie K. Wyllie, Michael J. Grillo, Clare K. Morris, Sophia P. Hirakis +6 more

Targeting N-Myc in neuroblastoma with selective Aurora kinase A degraders

Cell chemical biology(2025)10.1016/j.chembiol.2024.12.006

N/A

0DataRank · unranked

23 citations

Ramkumar Moorthy, Laura Hirsch, Özlem Demir, Zachary D. Baker, Jordan A. Naumann +12 more

In silico Drug Discovery: Bridging the Gaps in Preclinical Translation

Drug Discovery Today(2025)10.1016/j.drudis.2025.104567

N/A

0DataRank · unranked

3 citations

Hannah M. Baskir, A Grossman, Suchismita Chandran, Shyam Rele, Matthew D. Hall +4 more

Markovian state models uncover casein kinase 1 dynamics that govern circadian period

Biophysical Journal(2025)10.1016/j.bpj.2025.09.022

N/A

0DataRank · unranked

2 citations

Jonathan M. Philpott, Megan R Torgrimson, Alfred M. Freeberg, Rajesh Narasimamurthy, Emília P. Barros +5 more

An in vitro platform for the enzymatic characterization of the rhomboid protease RHBDL4

Journal of Biological Chemistry(2025)10.1016/j.jbc.2025.108275

N/A

0DataRank · unranked

2 citations

Mac Kevin E. Braza, Stancho Stanchev, Marina Tauber, Raghad Al-Bawab, Lawrence J. Liu +10 more

Nootropic benzothiazoles promote dendritic spine formation by targeting fascin-1

Journal of Biological Chemistry(2025)10.1016/j.jbc.2025.110572

N/A

0DataRank · unranked

1 citations

Kyle R. Berg, Kevin Carlo Abril Sibucao, Geoffray Leriche, Lara E. Dozier, Carla A. Espinoza +12 more

Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.17.633651

N/A

0DataRank · unranked

1 citations

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