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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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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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Polypolish: Short-read polishing of long-read bacterial genome assemblies

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009802-e1009802

2022

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

Viruses, 2020-05, Vol.12 (5), p.497

2020

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ProMod3-A versatile homology modelling toolbox

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008667-e1008667

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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Two-dimensional video-based analysis of human gait using pose estimation

PLoS computational biology, 2021-04, Vol.17 (4), p.e1008935-e1008935

2021

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Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

eLife, 2016-10, Vol.5

2016

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Integrative Structure Modeling: Overview and Assessment

Annual review of biochemistry, 2019-06, Vol.88, p.113

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

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

2022

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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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A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

PLoS computational biology, 2022-05, Vol.18 (5), p.e1009123-e1009123

2022

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DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006718-e1006718

2019

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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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PEtab-Interoperable specification of parameter estimation problems in systems biology

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008646

2021

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OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics

PLoS computational biology, 2022-11, Vol.18 (11), p.e1010584-e1010584

2022

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006971-e1006971

2019

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DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008374-e1008374

2021

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BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

PLoS computational biology, 2020-11, Vol.16 (11), p.e1008444-e1008444

2020

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ProteinVR: Web-based molecular visualization in virtual reality

PLoS computational biology, 2020-03, Vol.16 (3), p.e1007747-e1007747

2020

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Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

PLoS computational biology, 2022-04, Vol.18 (4), p.e1009578-e1009578

2022

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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

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

Polypolish: Short-read polishing of long-read bacterial genome assemblies

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

ProMod3-A versatile homology modelling toolbox

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Two-dimensional video-based analysis of human gait using pose estimation

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

Integrative Structure Modeling: Overview and Assessment

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

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

Uncertainty in integrative structural modeling

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network

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

PEtab-Interoperable specification of parameter estimation problems in systems biology

CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation

OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

ProteinVR: Web-based molecular visualization in virtual reality

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

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