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1
UniProt: the Universal Protein Knowledgebase in 2023
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UniProt: the Universal Protein Knowledgebase in 2023

Nucleic acids research, 2023-01, Vol.51 (D1), p.D523-D531 [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkac1052 ;PMID: 36408920

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2
CDD/SPARCLE: the conserved domain database in 2020
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CDD/SPARCLE: the conserved domain database in 2020

Nucleic acids research, 2020-01, Vol.48 (D1), p.D265-D268 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2019. 2019 ;Published by Oxford University Press on behalf of Nucleic Acids Research 2019. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz991 ;PMID: 31777944

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3
Protein sequence design with a learned potential
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Protein sequence design with a learned potential

Nature communications, 2022-02, Vol.13 (1), p.746-746, Article 746 [Peer Reviewed Journal]

2022. The Author(s). ;The Author(s) 2022. 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) 2022 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-022-28313-9 ;PMID: 35136054

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4
The InterPro protein families and domains database: 20 years on
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The InterPro protein families and domains database: 20 years on

Nucleic Acids Research, 2021-01, Vol.49 (D1), p.D344-D354 [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. ;2020. 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. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkaa977 ;PMID: 33156333

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5
InterPro in 2022
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InterPro in 2022

Nucleic acids research, 2023-01, Vol.51 (D1), p.D418-D427 [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkac993 ;PMID: 36350672

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6
Fast and sensitive taxonomic classification for metagenomics with Kaiju
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Fast and sensitive taxonomic classification for metagenomics with Kaiju

Nature communications, 2016-04, Vol.7 (1), p.11257-11257, Article 11257 [Peer Reviewed Journal]

Copyright Nature Publishing Group Apr 2016 ;Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/ncomms11257 ;PMID: 27071849

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7
A crowdsourcing open platform for literature curation in UniProt
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A crowdsourcing open platform for literature curation in UniProt

PLoS biology, 2021-12, Vol.19 (12), p.e3001464-e3001464 [Peer Reviewed Journal]

2021 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2021 Wang et al 2021 Wang et al ;ISSN: 1545-7885 ;ISSN: 1544-9173 ;EISSN: 1545-7885 ;DOI: 10.1371/journal.pbio.3001464 ;PMID: 34871295

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8
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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9
Accurately clustering biological sequences in linear time by relatedness sorting
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Accurately clustering biological sequences in linear time by relatedness sorting

Nature communications, 2024-04, Vol.15 (1), p.3047-3047 [Peer Reviewed Journal]

2024. The Author(s). ;The Author(s) 2024. 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) 2024 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-024-47371-9 ;PMID: 38589369

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10
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Nucleic acids research, 2022-01, Vol.50 (D1), p.D439-D444 [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/gkab1061 ;PMID: 34791371

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11
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Nucleic acids research, 2022-01, Vol.50 (D1), p.D543-D552 [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/gkab1038 ;PMID: 34723319

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12
ProtGPT2 is a deep unsupervised language model for protein design
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ProtGPT2 is a deep unsupervised language model for protein design

Nature communications, 2022-07, Vol.13 (1), p.4348-4348, Article 4348 [Peer Reviewed Journal]

The Author(s) 2022. 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) 2022 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-022-32007-7 ;PMID: 35896542

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13
MAFFT-DASH: integrated protein sequence and structural alignment
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MAFFT-DASH: integrated protein sequence and structural alignment

Nucleic acids research, 2019-07, Vol.47 (W1), p.W5-W10 [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/gkz342 ;PMID: 31062021

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14
KEGG as a reference resource for gene and protein annotation
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Article
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KEGG as a reference resource for gene and protein annotation

Nucleic acids research, 2016-01, Vol.44 (D1), p.D457-D462 [Peer Reviewed Journal]

The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 2016 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkv1070 ;PMID: 26476454

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15
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Scientific reports, 2021-06, Vol.11 (1), p.12728-12728, Article 12728 [Peer Reviewed Journal]

This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 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. ;This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021 ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/s41598-021-91456-0 ;PMID: 34135355

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16
CDD: NCBI's conserved domain database
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CDD: NCBI's conserved domain database

Nucleic acids research, 2015-01, Vol.43 (Database issue), p.D222-D226 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US. ;Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US. 2015 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gku1221 ;PMID: 25414356

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17
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules
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SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules

Nucleic acids research, 2019-07, Vol.47 (W1), p.W357-W364 [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/gkz382 ;PMID: 31106366

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18
BRENDA in 2019: a European ELIXIR core data resource
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BRENDA in 2019: a European ELIXIR core data resource

Nucleic acids research, 2019-01, Vol.47 (D1), p.D542-D549 [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/gky1048 ;PMID: 30395242

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19
HydDB: A web tool for hydrogenase classification and analysis
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HydDB: A web tool for hydrogenase classification and analysis

Scientific reports, 2016-09, Vol.6 (1), p.34212-34212, Article 34212 [Peer Reviewed Journal]

Copyright Nature Publishing Group Sep 2016 ;Copyright © 2016, The Author(s) 2016 The Author(s) ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/srep34212 ;PMID: 27670643

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20
A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold
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Article
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A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold

Nature communications, 2019-04, Vol.10 (1), p.1864-1864, Article 1864 [Peer Reviewed Journal]

The Author(s) 2019. 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/s41467-019-09836-0 ;PMID: 31015551

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