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Kolodny, Rachel
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1

Infer global, predict local: Quantity-relevance trade-off i..:

Posani, Lorenzo ; Rizzato, Francesca ; Monasson, Rémi..
PLOS Computational Biology.  19 (2023)  10 - p. e1011521 , 2023
Link: https://doi.org/10.1371/..
 
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2

An objective criterion to evaluate sequence-similarity netw..:

Hornung, Bastian Volker Helmut ; Terrapon, Nicolas ; Kolodny, Rachel
PLOS Computational Biology.  19 (2023)  8 - p. e1010881 , 2023
Link: https://doi.org/10.1371/..
 
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3

What can AlphaFold do for antimicrobial amyloids?:

Ragonis‐Bachar, Peleg ; Axel, Gabriel ; Blau, Shahar...
Proteins: Structure, Function, and Bioinformatics.  92 (2023)  2 - p. 265-281 , 2023
Link: https://doi.org/10.1002/..
 
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4

Machine learning modeling of family wide enzyme-substrate s..:

Goldman, Samuel ; Das, Ria ; Yang, Kevin K...
PLOS Computational Biology.  18 (2022)  2 - p. e1009853 , 2022
Link: https://doi.org/10.1371/..
 
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5

From complete cross-docking to partners identification and ..:

Dequeker, Chloé ; Mohseni Behbahani, Yasser ; David, Laurent...
PLOS Computational Biology.  18 (2022)  1 - p. e1009825 , 2022
Link: https://doi.org/10.1371/..
 
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6

Adventures on the Routes of Protein Evolution—In Memoriam D..:

Jackson, Colin ; Toth-Petroczy, Agnes ; Kolodny, Rachel...
Journal of Molecular Biology.  434 (2022)  7 - p. 167462 , 2022
Link: https://doi.org/10.1016/..
 
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7

Inter-paralog amino acid inversion events in large phylogen..:

Pascarelli, Stefano ; Laurino, Paola ; Kolodny, Rachel
PLOS Computational Biology.  18 (2022)  4 - p. e1010016 , 2022
Link: https://doi.org/10.1371/..
 
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8

Evidence for the emergence of β-trefoils by 'Peptide Buddin..:

Longo, Liam M. ; Kolodny, Rachel ; McGlynn, Shawn E..
PLOS Computational Biology.  18 (2022)  2 - p. e1009833 , 2022
Link: https://doi.org/10.1371/..
 
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9

Annotation-free delineation of prokaryotic homology groups:

Yin, Yongze ; Ogilvie, Huw A. ; Nakhleh, Luay.
PLOS Computational Biology.  18 (2022)  6 - p. e1010216 , 2022
Link: https://doi.org/10.1371/..
 
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10

Homologues not needed: Structure prediction from a protein ..:

Ben-Tal, Nir ; Kolodny, Rachel
Structure.  30 (2022)  8 - p. 1047-1049 , 2022
Link: https://doi.org/10.1016/..
 
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11

Similar protein segments shared between domains of differen..:

Qiu, Kaiyu ; Ben‐Tal, Nir ; Kolodny, Rachel
Protein Science.  31 (2022)  9 - p. , 2022
Link: https://doi.org/10.1002/..
 
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12

Bridging Themes: Short Protein Segments Found in Different ..:

Kolodny, Rachel ; Nepomnyachiy, Sergey ; Tawfik, Dan S..
Molecular Biology and Evolution.  38 (2021)  6 - p. 2191-2208 , 2021
Link: https://doi.org/10.1093/..
 
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13

Hybridized distance- and contact-based hierarchical structu..:

Roche, Rahmatullah ; Bhattacharya, Sutanu ; Bhattacharya, Debswapna.
PLOS Computational Biology.  17 (2021)  2 - p. e1008753 , 2021
Link: https://doi.org/10.1371/..
 
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14

Deducing high-accuracy protein contact-maps from a triplet ..:

Li, Yang ; Zhang, Chengxin ; Bell, Eric W....
PLOS Computational Biology.  17 (2021)  3 - p. e1008865 , 2021
Link: https://doi.org/10.1371/..
 
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15

How Deep Learning Tools Can Help Protein Engineers Find Goo..:

Osadchy, Margarita ; Kolodny, Rachel
The Journal of Physical Chemistry B.  125 (2021)  24 - p. 6440-6450 , 2021
Link: https://doi.org/10.1021/..
 
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