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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

The international journal of high performance computing applications, 2021-09, Vol.35 (5), p.432-451

2021

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

Biophysical journal, 2021-03, Vol.120 (6), p.1072-1084

2021

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

ACS central science, 2020-10, Vol.6 (10), p.1722-1734

2020

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D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

Journal of computer-aided molecular design, 2020-02, Vol.34 (2), p.99-119

2020

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D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

Journal of computer-aided molecular design, 2019-01, Vol.33 (1), p.1-18

2019

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D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

Journal of computer-aided molecular design, 2018-01, Vol.32 (1), p.1-20

2018

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

eLife, 2021-03, Vol.10

2021

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Dissecting Distinct Roles of NEDDylation E1 Ligase Heterodimer APPBP1 and UBA3 Reveals Potential Evolution Process for Activation of Ubiquitin-related Pathways

Scientific reports, 2018-07, Vol.8 (1), p.10108-10, Article 10108

2018

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Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

Computational and structural biotechnology journal, 2017-01, Vol.15, p.131-137

2017

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

Frontiers in molecular biosciences, 2020-06, Vol.7, p.93-93

2020

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Comparison of commonly used solid tumor targeted gene sequencing panels for estimating tumor mutation burden shows analytical and prognostic concordance within the cancer genome atlas cohort

Journal for immunotherapy of cancer, 2020-03, Vol.8 (1), p.e000613

2020

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Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition

Frontiers in molecular biosciences, 2021-03, Vol.8, p.618068-618068

2021

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Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding

Journal of molecular graphics & modelling, 2017-06, Vol.74, p.352-358

2017

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A multiscale coarse-grained model of the SARS-CoV-2 virion

Biophysical journal, 2021-03, Vol.120 (6), p.1097-1104

2021

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Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7

Journal of chemical information and modeling, 2016-09, Vol.56 (9), p.1808-1822

2016

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Ligand-Specific Conformational Changes in CCR7 Coupled to Selecting Different Signaling Pathways upon CCL19 And CCL21 Ligand Binding

Biophysical journal, 2016-02, Vol.110 (3), p.361a-361a

2016

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

Biophysical journal, 2021-03, Vol.120 (6), p.983-993

2021

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Electrostatic Interactions between Complement Regulator CD46(SCR1-2) and Adenovirus Ad11/Ad21 Fiber Protein Knob

Molecular Biology International, 2015-01, Vol.2015, p.54-68

2015

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

Journal of medicinal chemistry, 2021-05, Vol.64 (9), p.5787-5801

2021

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SARS-CoV-2 Glycosylated Spike Activation Mechanism - Simulations of the Full Unbiased Pathway

Biophysical journal, 2021-02, Vol.120 (3), p.276a-276a

2021

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Dual Inhibitors of Cyclooxygenase‐2 and Soluble Epoxide Hydrolase: Studies of Binding Modes at the Active Sites and Time‐dependency of Inhibition, and Development of Water‐soluble Prodrugs

The FASEB journal, 2018-04, Vol.32 (S1), p.558.2-558.2

2018

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Disease-related mutations in PI3K[gamma] disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors

eLife, 2021-03, Vol.10

2021

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Molecular Switches Coordinate Dynamically Coupled Allosteric Networks in Protein Complexes

Gaieb, Zied

2016

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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

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

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

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

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

Dissecting Distinct Roles of NEDDylation E1 Ligase Heterodimer APPBP1 and UBA3 Reveals Potential Evolution Process for Activation of Ubiquitin-related Pathways

Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors

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

Comparison of commonly used solid tumor targeted gene sequencing panels for estimating tumor mutation burden shows analytical and prognostic concordance within the cancer genome atlas cohort

Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition

Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding

A multiscale coarse-grained model of the SARS-CoV-2 virion

Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7

Ligand-Specific Conformational Changes in CCR7 Coupled to Selecting Different Signaling Pathways upon CCL19 And CCL21 Ligand Binding

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

Electrostatic Interactions between Complement Regulator CD46(SCR1-2) and Adenovirus Ad11/Ad21 Fiber Protein Knob

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

SARS-CoV-2 Glycosylated Spike Activation Mechanism - Simulations of the Full Unbiased Pathway

Dual Inhibitors of Cyclooxygenase‐2 and Soluble Epoxide Hydrolase: Studies of Binding Modes at the Active Sites and Time‐dependency of Inhibition, and Development of Water‐soluble Prodrugs

Disease-related mutations in PI3K[gamma] disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors

Molecular Switches Coordinate Dynamically Coupled Allosteric Networks in Protein Complexes

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