Yusuf Hamied Department of Chemistry

Publications by Dr Lucy Colwell

InterPro: The protein sequence classification resource in 2025
M Blum, A Andreeva, LC Florentino, SR Chuguransky, T Grego, E Hobbs, BL Pinto, A Orr, T Paysan-Lafosse, I Ponamareva, GA Salazar, N Bordin, P Bork, A Bridge, L Colwell, J Gough, DH Haft, I Letunic, F Llinares-López, A Marchler-Bauer, L Meng-Papaxanthos, H Mi, DA Natale, CA Orengo, AP Pandurangan, D Piovesan, C Rivoire, CJA Sigrist, N Thanki, F Thibaud-Nissen, PD Thomas, SCE Tosatto, CH Wu, A Bateman
Nucleic Acids Research
(2024)
53
(doi: 10.1093/nar/gkae1082)
Investigation of protein family relationships with deep learning
I Ponamareva, A Andreeva, ML Bileschi, L Colwell, A Bateman
Bioinformatics Advances
(2024)
4
(doi: 10.1093/bioadv/vbae132)
Machine learning designs new GCGR/GLP-1R dual agonists with enhanced biological potency.
AM Puszkarska, B Taddese, J Revell, G Davies, J Field, DC Hornigold, A Buchanan, TJ Vaughan, LJ Colwell
Nature Chemistry
(2024)
16
(doi: 10.1038/s41557-024-01532-x)
Predicting multiple conformations via sequence clustering and AlphaFold2.
HK Wayment-Steele, A Ojoawo, R Otten, JM Apitz, W Pitsawong, M Hömberger, S Ovchinnikov, L Colwell, D Kern
Nature
(2023)
625
(doi: 10.1038/s41586-023-06832-9)
ProteInfer, deep neural networks for protein functional inference
T Sanderson, ML Bileschi, D Belanger, LJ Colwell
eLife
(2023)
12
(doi: 10.7554/eLife.80942)
Hallucinating functional protein sequences
D Belanger, LJ Colwell
Nature Biotechnology
(2023)
41
(doi: 10.1038/s41587-022-01634-2)
InterPro in 2022.
T Paysan-Lafosse, M Blum, S Chuguransky, T Grego, BL Pinto, GA Salazar, ML Bileschi, P Bork, A Bridge, L Colwell, J Gough, DH Haft, I Letunić, A Marchler-Bauer, H Mi, DA Natale, CA Orengo, AP Pandurangan, C Rivoire, CJA Sigrist, I Sillitoe, N Thanki, PD Thomas, SCE Tosatto, CH Wu, A Bateman
Nucleic Acids Res
(2022)
51
(doi: 10.1093/nar/gkac993)
Prediction of multiple conformational states by combining sequence clustering with AlphaFold2
HK Wayment-Steele, S Ovchinnikov, L Colwell, D Kern
(2022)
(doi: 10.1101/2022.10.17.512570)
Using deep learning to annotate the protein universe.
ML Bileschi, D Belanger, DH Bryant, T Sanderson, B Carter, D Sculley, A Bateman, MA DePristo, LJ Colwell
Nature biotechnology
(2022)
40
(doi: 10.1038/s41587-021-01179-w)
Minding the gaps: The importance of navigating holes in protein fitness landscapes
N Thomas, LJ Colwell
Cell Systems
(2021)
12
(doi: 10.1016/j.cels.2021.10.004)
ProteInfer: deep networks for protein functional inference
T Sanderson, ML Bileschi, D Belanger, LJ Colwell
(2021)
(doi: 10.1101/2021.09.20.461077)
Deep diversification of an AAV capsid protein by machine learning.
DH Bryant, A Bashir, S Sinai, NK Jain, PJ Ogden, PF Riley, GM Church, LJ Colwell, ED Kelsic
Nature Biotechnology
(2021)
39
(doi: 10.1038/s41587-020-00793-4)
Using Single Protein/Ligand Binding Models to Predict Active Ligands for Unseen Proteins
V Sundar, L Colwell
(2020)
(doi: 10.1101/2020.08.02.233155)
Critiquing Protein Family Classification Models Using Sufficient Input Subsets.
B Carter, M Bileschi, J Smith, T Sanderson, D Bryant, D Belanger, LJ Colwell
J Comput Biol
(2020)
27
(doi: 10.1089/cmb.2019.0339)
Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase-tRNA pairs
D Cervettini, S Tang, SD Fried, JCW Willis, LFH Funke, LJ Colwell, JW Chin
Nature Biotechnology
(2020)
38
(doi: 10.1038/s41587-020-0479-2)
Glycation changes molecular organization and charge distribution in type I collagen fibrils.
S Bansode, U Bashtanova, R Li, J Clark, KH Müller, A Puszkarska, I Goldberga, HH Chetwood, DG Reid, LJ Colwell, JN Skepper, CM Shanahan, G Schitter, P Mesquida, MJ Duer
Scientific Reports
(2020)
10
(doi: 10.1038/s41598-020-60250-9)
Collagen-Inspired Self-Assembly of Twisted Filaments
MJ Falk, A Duwel, LJ Colwell, MP Brenner
Physical Review Letters
(2019)
123
(doi: 10.1103/physrevlett.123.238102)
Computational approaches to therapeutic antibody design: established methods and emerging trends.
RA Norman, F Ambrosetti, AMJJ Bonvin, LJ Colwell, S Kelm, S Kumar, K Krawczyk
Briefings in Bioinformatics
(2019)
21
(doi: 10.1093/bib/bbz095)
A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.
O Kimchi, T Cragnolini, MP Brenner, LJ Colwell
Biophysical Journal
(2019)
117
(doi: 10.1016/j.bpj.2019.06.037)
Critiquing Protein Family Classification Models Using Sufficient Input Subsets
B Carter, M Bileschi, J Smith, T Sanderson, D Bryant, D Belanger, L Colwell
(2019)
(doi: 10.1101/674119)
Yusuf Hamied Department of Chemistry
Lensfield Road
Cambridge
CB2 1EW
T: +44 (0) 1223 336300
enquiries@ch.cam.ac.uk
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