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Searching protein space for ancient sub-domain segments

Current opinion in structural biology, 2021-06, Vol.68, p.105-112

Kolodny, Rachel

2021

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How Deep Learning Tools Can Help Protein Engineers Find Good Sequences

The journal of physical chemistry. B, 2021-06, Vol.125 (24), p.6440-6450

2021

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Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008865-e1008865

2021

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Machine learning modeling of family wide enzyme-substrate specificity screens

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009853-e1009853

2022

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Bridging Themes: Short Protein Segments Found in Different Architectures

Molecular biology and evolution, 2021-05, Vol.38 (6), p.2191-2208

2021

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Similar protein segments shared between domains of different evolutionary lineages

Protein science, 2022-09, Vol.31 (9), p.e4407-n/a

2022

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Global view of the protein universe

Proceedings of the National Academy of Sciences - PNAS, 2014-08, Vol.111 (32), p.11691-11696

2014

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Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009833-e1009833

2022

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Maps of protein structure space reveal a fundamental relationship between protein structure and function

Proceedings of the National Academy of Sciences - PNAS, 2011-07, Vol.108 (30), p.12301-12306

2011

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In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species

PLoS computational biology, 2020-12, Vol.16 (12), p.e1008450

2020

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FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately

Proceedings of the National Academy of Sciences - PNAS, 2010-02, Vol.107 (8), p.3481-3486

2010

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Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data

PLoS computational biology, 2023-10, Vol.19 (10), p.e1011521-e1011521

2023

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An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space

PLoS computational biology, 2023-08, Vol.19 (8), p.e1010881-e1010881

2023

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Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

Journal of molecular biology, 2005-03, Vol.346 (4), p.1173-1188

2005

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On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment

eLife, 2020-12, Vol.9

2020

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From complete cross-docking to partners identification and binding sites predictions

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009825-e1009825

2022

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A global map of the protein shape universe

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006969-e1006969

2019

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Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins

PLoS computational biology, 2022-04, Vol.18 (4), p.e1010016-e1010016

2022

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Annotation-free delineation of prokaryotic homology groups

PLoS computational biology, 2022-06, Vol.18 (6), p.e1010216-e1010216

2022

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Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008753-e1008753

2021

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In Silico Structural and Biochemical Functional Analysis of a Novel CYP21A2 Pathogenic Variant

International journal of molecular sciences, 2020-08, Vol.21 (16), p.5857

2020

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Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

eLife, 2018-11, Vol.7

2018

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Approximate Protein Structural Alignment in Polynomial Time

Proceedings of the National Academy of Sciences - PNAS, 2004-08, Vol.101 (33), p.12201-12206

2004

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Small Libraries of Protein Fragments Model Native Protein Structures Accurately

Journal of molecular biology, 2002-10, Vol.323 (2), p.297-307

2002

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Homologues not needed: Structure prediction from a protein language model

Structure (London), 2022-08, Vol.30 (8), p.1047-1049

2022

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Searching protein space for ancient sub-domain segments

How Deep Learning Tools Can Help Protein Engineers Find Good Sequences

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

Machine learning modeling of family wide enzyme-substrate specificity screens

Bridging Themes: Short Protein Segments Found in Different Architectures

Similar protein segments shared between domains of different evolutionary lineages

Global view of the protein universe

Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich

Maps of protein structure space reveal a fundamental relationship between protein structure and function

In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately

Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data

An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space

Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment

From complete cross-docking to partners identification and binding sites predictions

A global map of the protein shape universe

Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins

Annotation-free delineation of prokaryotic homology groups

Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins

In Silico Structural and Biochemical Functional Analysis of a Novel CYP21A2 Pathogenic Variant

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Approximate Protein Structural Alignment in Polynomial Time

Small Libraries of Protein Fragments Model Native Protein Structures Accurately

Homologues not needed: Structure prediction from a protein language model

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