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1
ECNet is an evolutionary context-integrated deep learning framework for protein engineering
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ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Nature communications, 2021-09, Vol.12 (1), p.5743-14, Article 5743 [Peer Reviewed Journal]

2021. The Author(s). ;The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2021 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-021-25976-8 ;PMID: 34593817

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2
The PSIPRED Protein Analysis Workbench: 20 years on
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The PSIPRED Protein Analysis Workbench: 20 years on

Nucleic acids research, 2019-07, Vol.47 (W1), p.W402-W407 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz297 ;PMID: 31251384

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3
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
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ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

Nucleic acids research, 2016-07, Vol.44 (W1), p.W344-W350 [Peer Reviewed Journal]

The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. 2016 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkw408 ;PMID: 27166375

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4
CATH: increased structural coverage of functional space
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CATH: increased structural coverage of functional space

Nucleic acids research, 2021-01, Vol.49 (D1), p.D266-D273 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021 ;The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkaa1079 ;PMID: 33237325

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5
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
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ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Nucleic acids research, 2010-07, Vol.38 (Web Server issue), p.W529-W533 [Peer Reviewed Journal]

The Author(s) 2010. Published by Oxford University Press. 2010 ;ISSN: 0305-1048 ;ISSN: 1362-4962 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkq399 ;PMID: 20478830

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6
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity
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VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

Nucleic acids research, 2018-01, Vol.46 (D1), p.D419-D427 [Peer Reviewed Journal]

The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 ;The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkx760 ;PMID: 28977646

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7
Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation
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Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation

Nature communications, 2018-01, Vol.9 (1), p.382-12, Article 382 [Peer Reviewed Journal]

2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2018 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-018-02881-1 ;PMID: 29374183

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8
Embeddings from deep learning transfer GO annotations beyond homology
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Embeddings from deep learning transfer GO annotations beyond homology

Scientific reports, 2021-01, Vol.11 (1), p.1160-1160, Article 1160 [Peer Reviewed Journal]

The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2021 ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/s41598-020-80786-0 ;PMID: 33441905

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9
The Pfam protein families database
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The Pfam protein families database

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D211-D222 [Peer Reviewed Journal]

The Author(s) 2009. Published by Oxford University Press. 2009 ;ISSN: 0305-1048 ;ISSN: 1362-4962 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkp985 ;PMID: 19920124

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10
Global phosphoproteomic analysis reveals ARMC10 as an AMPK substrate that regulates mitochondrial dynamics
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Global phosphoproteomic analysis reveals ARMC10 as an AMPK substrate that regulates mitochondrial dynamics

Nature communications, 2019-01, Vol.10 (1), p.104-104, Article 104 [Peer Reviewed Journal]

This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2019 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-018-08004-0 ;PMID: 30631047

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11
CATH: expanding the horizons of structure-based functional annotations for genome sequences
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CATH: expanding the horizons of structure-based functional annotations for genome sequences

Nucleic acids research, 2019-01, Vol.47 (D1), p.D280-D284 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gky1097 ;PMID: 30398663

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12
NetGO: improving large-scale protein function prediction with massive network information
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NetGO: improving large-scale protein function prediction with massive network information

Nucleic acids research, 2019-07, Vol.47 (W1), p.W379-W387 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz388 ;PMID: 31106361

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13
The current state of SubtiWiki, the database for the model organism Bacillus subtilis
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The current state of SubtiWiki, the database for the model organism Bacillus subtilis

Nucleic acids research, 2022-01, Vol.50 (D1), p.D875-D882 [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022 ;The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkab943 ;PMID: 34664671

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14
ComplexContact: a web server for inter-protein contact prediction using deep learning
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ComplexContact: a web server for inter-protein contact prediction using deep learning

Nucleic acids research, 2018-07, Vol.46 (W1), p.W432-W437 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gky420 ;PMID: 29790960

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15
IntFOLD: an integrated web resource for high performance protein structure and function prediction
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IntFOLD: an integrated web resource for high performance protein structure and function prediction

Nucleic acids research, 2019-07, Vol.47 (W1), p.W408-W413 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz322 ;PMID: 31045208

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16
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment
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DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

BMC bioinformatics, 2015-10, Vol.16 (1), p.322-322, Article 322 [Peer Reviewed Journal]

COPYRIGHT 2015 BioMed Central Ltd. ;Copyright BioMed Central 2015 ;Wright. 2015 ;ISSN: 1471-2105 ;EISSN: 1471-2105 ;DOI: 10.1186/s12859-015-0749-z ;PMID: 26445311

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17
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination
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AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

Nucleic acids research, 2018-07, Vol.46 (W1), p.W479-W485 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gky359 ;PMID: 29762724

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18
Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour
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Article
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Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour

Nature communications, 2014-06, Vol.5 (1), p.4039-4039, Article 4039 [Peer Reviewed Journal]

Copyright Nature Publishing Group Jun 2014 ;Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/ncomms5039 ;PMID: 24909261

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19
Mini-G proteins: Novel tools for studying GPCRs in their active conformation
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Mini-G proteins: Novel tools for studying GPCRs in their active conformation

PloS one, 2017-04, Vol.12 (4), p.e0175642-e0175642 [Peer Reviewed Journal]

COPYRIGHT 2017 Public Library of Science ;This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0175642 ;PMID: 28426733

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20
Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
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Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

BMC bioinformatics, 2018-05, Vol.19 (1), p.189-189, Article 189 [Peer Reviewed Journal]

COPYRIGHT 2018 BioMed Central Ltd. ;Copyright © 2018. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2018 ;ISSN: 1471-2105 ;EISSN: 1471-2105 ;DOI: 10.1186/s12859-018-2203-5 ;PMID: 29843602

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