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Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

PLoS computational biology, 2015-07, Vol.11 (7), p.e1004404-e1004404

2015

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Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities

PloS one, 2014-09, Vol.9 (9), p.e108928

2014

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Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

RNA (Cambridge), 2011-06, Vol.17 (6), p.1066-1075

2011

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GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies

PloS one, 2015-08, Vol.10 (8), p.e0136444-e0136444

2015

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DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions

Bioinformatics, 2008-03, Vol.24 (5), p.652-658

2008

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Catalytic Mechanism and Structure of Viral Flavin-dependent Thymidylate Synthase ThyX

The Journal of biological chemistry, 2006-08, Vol.281 (33), p.24048-24057

2006

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Modeling Protein-RNA Complexes

Biophysical journal, 2016-02, Vol.110 (3), p.241a-241a

2016

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GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization

Bioinformatics (Oxford, England), 2017-08, Vol.33 (16), p.2479-2486

2017

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Probing RNA Native Conformational Ensembles with Structural Constraints

Journal of computational biology, 2016-05, Vol.23 (5), p.362-371

2016

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Coupled Motions in β2AR:Gαs Conformational Ensembles

Journal of chemical theory and computation, 2016-03, Vol.12 (3), p.946-956

2016

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Characterizing RNA ensembles from NMR data with kinematic models

Nucleic acids research, 2014-09, Vol.42 (15), p.9562-9572

2014

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Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1517, p.251

2017

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Coupled Motions in β 2 AR:Gαs Conformational Ensembles

Journal of chemical theory and computation, 2016-03, Vol.12 (3), p.946-956

2016

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Coupled Motions in [beta] sub(2) AR:G[alpha]s Conformational Ensembles

Journal of chemical theory and computation, 2016-03, Vol.12 (3), p.946-956

2016

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Efficient large-scale language model training on GPU clusters using megatron-LM

Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2021, p.1-15

2021

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Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement: e1004404

PLoS computational biology, 2015-07, Vol.11 (7)

2015

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A new protein-protein docking scoring function based on interface residue properties

Bioinformatics, 2007-03, Vol.23 (5), p.555-562

2007

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A Protein-RNA Knowledge-Based Potential for Scoring and Refinement

Biophysical journal, 2014-01, Vol.106 (2), p.699a-699a

2014

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Multiscale modeling of macromolecular biosystems

Briefings in bioinformatics, 2012-07, Vol.13 (4), p.395-405

2012

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ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules

Bioinformatics, 2010-04, Vol.26 (8), p.1127-1128

2010

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In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution

RNA (Cambridge), 2014-10, Vol.20 (10), p.1607-1620

2014

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In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution

RNA (Cambridge), 2014-11, Vol.20 (11), p.1827-1827

2014

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GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies: e0136444

PloS one, 2015-08, Vol.10 (8)

2015

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NVIDIA Deep Learning Tutorial

2017 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2017, p.491-491

Bernauer, Julie

2017

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Multiscale modeling of macromolecular biosystems: Current Progress in Bioinformatics 2012

Briefings in bioinformatics, 2012, Vol.13 (4), p.395-405

2012

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Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies

DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions

Catalytic Mechanism and Structure of Viral Flavin-dependent Thymidylate Synthase ThyX

Modeling Protein-RNA Complexes

GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization

Probing RNA Native Conformational Ensembles with Structural Constraints

Coupled Motions in β2AR:Gαs Conformational Ensembles

Characterizing RNA ensembles from NMR data with kinematic models

Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches

Coupled Motions in β 2 AR:Gαs Conformational Ensembles

Coupled Motions in [beta] sub(2) AR:G[alpha]s Conformational Ensembles

Efficient large-scale language model training on GPU clusters using megatron-LM

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement: e1004404

A new protein-protein docking scoring function based on interface residue properties

A Protein-RNA Knowledge-Based Potential for Scoring and Refinement

Multiscale modeling of macromolecular biosystems

ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules

In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution

In vivo tmRNA protection by SmpB and pre-ribosome binding conformation in solution

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies: e0136444

NVIDIA Deep Learning Tutorial

Multiscale modeling of macromolecular biosystems: Current Progress in Bioinformatics 2012

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