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A deep learning model for predicting optimal distance range in crosslinking mass spectrometry data

Proteomics (Weinheim), 2023-09, Vol.23 (17), p.e2200341-n/a

2023

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Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Nature communications, 2021-08, Vol.12 (1), p.4676-4676, Article 4676

2021

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Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Science (American Association for the Advancement of Science), 2020-12, Vol.370 (6523), p.1479-1484

2020

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The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

Viruses, 2020-04, Vol.12 (5), p.497

2020

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Dissecting peripheral protein-membrane interfaces

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010346

2022

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Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

PLoS computational biology, 2024-07, Vol.20 (7), p.e1012253

2024

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NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning

Frontiers in immunology, 2022-08, Vol.13, p.958584

2022

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The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement

PLoS computational biology, 2023-11, Vol.19 (11), p.e1011248-e1011248

2023

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Integrative Structure Modeling: Overview and Assessment

Annual review of biochemistry, 2019-06, Vol.88 (1), p.113-135

2019

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Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

Biophysical journal, 2013-08, Vol.105 (4), p.962-974

2013

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Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution

PLoS computational biology, 2023-08, Vol.19 (8), p.e1011090-e1011090

2023

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Uncertainty in integrative structural modeling

Current opinion in structural biology, 2014-10, Vol.28, p.96-104

2014

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Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods

PLoS computational biology, 2022-12, Vol.18 (12), p.e1010230-e1010230

2022

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An integrated suite of fast docking algorithms

Proteins, structure, function, and bioinformatics, 2010-11, Vol.78 (15), p.3197-3204

2010

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De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A

American journal of medical genetics. Part B, Neuropsychiatric genetics, 2020-10, Vol.183 (7), p.412-422

2020

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Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

PLoS biology, 2012-01, Vol.10 (1), p.e1001244-e1001244

2012

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An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data

PLoS computational biology, 2018-03, Vol.14 (3), p.e1006054-e1006054

2018

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ModBase, a database of annotated comparative protein structure models and associated resources

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D336-D346

2014

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fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005838-e1005838

2017

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Integrative modelling of structure and dynamics of macromolecules based on SAXS profiles and cross-linking mass spectrometry

Acta crystallographica. Section A, Foundations and advances, 2021-08, Vol.77 (a2), p.C682-C682

Schneidman, Dina

2021

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φ-evo: A program to evolve phenotypic models of biological networks

PLoS computational biology, 2018-06, Vol.14 (6), p.e1006244-e1006244

2018

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CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

Journal of molecular biology, 2016-02, Vol.428 (4), p.709-719

2016

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Macromolecular docking restrained by a small angle X-ray scattering profile

Journal of structural biology, 2011-03, Vol.173 (3), p.461-471

2011

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Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data

Journal of the American Chemical Society, 2013-11, Vol.135 (44), p.16595-16609

2013

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Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2

Proceedings of the National Academy of Sciences - PNAS, 2021-08, Vol.118 (34), p.1

2021

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A deep learning model for predicting optimal distance range in crosslinking mass spectrometry data

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

Dissecting peripheral protein-membrane interfaces

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning

The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement

Integrative Structure Modeling: Overview and Assessment

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution

Uncertainty in integrative structural modeling

Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods

An integrated suite of fast docking algorithms

De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies

An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data

ModBase, a database of annotated comparative protein structure models and associated resources

fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks

Integrative modelling of structure and dynamics of macromolecules based on SAXS profiles and cross-linking mass spectrometry

φ-evo: A program to evolve phenotypic models of biological networks

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

Macromolecular docking restrained by a small angle X-ray scattering profile

Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data

Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2

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