Twenty Years of the MEROPS Database of Proteolytic Enzymes, Their Substrates and Inhibitors Neil D
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The ELIXIR Core Data Resources: Fundamental Infrastructure for The
Supplementary Data: The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences The “Supporting Material” referred to within this Supplementary Data can be found in the Supporting.Material.CDR.infrastructure file, DOI: 10.5281/zenodo.2625247 (https://zenodo.org/record/2625247). Figure 1. Scale of the Core Data Resources Table S1. Data from which Figure 1 is derived: Year 2013 2014 2015 2016 2017 Data entries 765881651 997794559 1726529931 1853429002 2715599247 Monthly user/IP addresses 1700660 2109586 2413724 2502617 2867265 FTEs 270 292.65 295.65 289.7 311.2 Figure 1 includes data from the following Core Data Resources: ArrayExpress, BRENDA, CATH, ChEBI, ChEMBL, EGA, ENA, Ensembl, Ensembl Genomes, EuropePMC, HPA, IntAct /MINT , InterPro, PDBe, PRIDE, SILVA, STRING, UniProt ● Note that Ensembl’s compute infrastructure physically relocated in 2016, so “Users/IP address” data are not available for that year. In this case, the 2015 numbers were rolled forward to 2016. ● Note that STRING makes only minor releases in 2014 and 2016, in that the interactions are re-computed, but the number of “Data entries” remains unchanged. The major releases that change the number of “Data entries” happened in 2013 and 2015. So, for “Data entries” , the number for 2013 was rolled forward to 2014, and the number for 2015 was rolled forward to 2016. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences 1 Figure 2: Usage of Core Data Resources in research The following steps were taken: 1. API calls were run on open access full text articles in Europe PMC to identify articles that mention Core Data Resource by name or include specific data record accession numbers. -
Deep Profiling of Protease Substrate Specificity Enabled by Dual Random and Scanned Human Proteome Substrate Phage Libraries
Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries Jie Zhoua, Shantao Lib, Kevin K. Leunga, Brian O’Donovanc, James Y. Zoub,d, Joseph L. DeRisic,d, and James A. Wellsa,d,e,1 aDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158; bDepartment of Biomedical Data Science, Stanford University, Stanford, CA 94305; cDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; dChan Zuckerberg Biohub, San Francisco, CA 94158; and eDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158 Edited by Benjamin F. Cravatt, Scripps Research Institute, La Jolla, CA, and approved August 19, 2020 (received for review May 11, 2020) Proteolysis is a major posttranslational regulator of biology inside lysate and miss low abundance proteins and those simply not and outside of cells. Broad identification of optimal cleavage sites expressed in cell lines tested that typically express only half their and natural substrates of proteases is critical for drug discovery genomes (13). and to understand protease biology. Here, we present a method To potentially screen a larger and more diverse sequence that employs two genetically encoded substrate phage display space, investigators have developed genetically encoded substrate libraries coupled with next generation sequencing (SPD-NGS) that phage (14, 15) or yeast display libraries (16, 17). Degenerate DNA allows up to 10,000-fold deeper sequence coverage of the typical six- sequences (up to 107) encoding random peptides were fused to a to eight-residue protease cleavage sites compared to state-of-the-art phage or yeast coat protein gene for a catch-and-release strategy synthetic peptide libraries or proteomics. -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
Methods in and Applications of the Sequencing of Short Non-Coding Rnas" (2013)
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Methods in and Applications of the Sequencing of Short Non- Coding RNAs Paul Ryvkin University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Ryvkin, Paul, "Methods in and Applications of the Sequencing of Short Non-Coding RNAs" (2013). Publicly Accessible Penn Dissertations. 922. https://repository.upenn.edu/edissertations/922 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/922 For more information, please contact [email protected]. Methods in and Applications of the Sequencing of Short Non-Coding RNAs Abstract Short non-coding RNAs are important for all domains of life. With the advent of modern molecular biology their applicability to medicine has become apparent in settings ranging from diagonistic biomarkers to therapeutics and fields angingr from oncology to neurology. In addition, a critical, recent technological development is high-throughput sequencing of nucleic acids. The convergence of modern biotechnology with developments in RNA biology presents opportunities in both basic research and medical settings. Here I present two novel methods for leveraging high-throughput sequencing in the study of short non- coding RNAs, as well as a study in which they are applied to Alzheimer's Disease (AD). The computational methods presented here include High-throughput Annotation of Modified Ribonucleotides (HAMR), which enables researchers to detect post-transcriptional covalent modifications ot RNAs in a high-throughput manner. In addition, I describe Classification of RNAs by Analysis of Length (CoRAL), a computational method that allows researchers to characterize the pathways responsible for short non-coding RNA biogenesis. -
Comparing Tools for Non-Coding RNA Multiple Sequence Alignment Based On
Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ES Wright 1 1 TITLE 2 RNAconTest: Comparing tools for non-coding RNA multiple sequence alignment based on 3 structural consistency 4 Running title: RNAconTest: benchmarking comparative RNA programs 5 Author: Erik S. Wright1,* 6 1 Department of Biomedical Informatics, University of Pittsburgh (Pittsburgh, PA) 7 * Corresponding author: Erik S. Wright ([email protected]) 8 Keywords: Multiple sequence alignment, Secondary structure prediction, Benchmark, non- 9 coding RNA, Consensus secondary structure 10 Downloaded from rnajournal.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press ES Wright 2 11 ABSTRACT 12 The importance of non-coding RNA sequences has become increasingly clear over the past 13 decade. New RNA families are often detected and analyzed using comparative methods based on 14 multiple sequence alignments. Accordingly, a number of programs have been developed for 15 aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for 16 these tasks remain unclear because existing benchmarks contain too few sequences belonging to 17 only a small number of RNA families. RNAconTest (RNA consistency test) is a new 18 benchmarking approach relying on the observation that secondary structure is often conserved 19 across highly divergent RNA sequences from the same family. RNAconTest scores multiple 20 sequence alignments based on the level of consistency among known secondary structures 21 belonging to reference sequences in their output alignment. Similarly, consensus secondary 22 structure predictions are scored according to their agreement with one or more known structures 23 in a family. -
Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I
EMBL-European Bioinformatics Institute Annual Scientific Report 2013 On the cover Structure 3fof in the Protein Data Bank, determined by Laponogov, I. et al. (2009) Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nature Structural & Molecular Biology 16, 667-669. © 2014 European Molecular Biology Laboratory This publication was produced by the External Relations team at the European Bioinformatics Institute (EMBL-EBI) A digital version of the brochure can be found at www.ebi.ac.uk/about/brochures For more information about EMBL-EBI please contact: [email protected] Contents Introduction & overview 3 Services 8 Genes, genomes and variation 8 Molecular atlas 12 Proteins and protein families 14 Molecular and cellular structures 18 Chemical biology 20 Molecular systems 22 Cross-domain tools and resources 24 Research 26 Support 32 ELIXIR 36 Facts and figures 38 Funding & resource allocation 38 Growth of core resources 40 Collaborations 42 Our staff in 2013 44 Scientific advisory committees 46 Major database collaborations 50 Publications 52 Organisation of EMBL-EBI leadership 61 2013 EMBL-EBI Annual Scientific Report 1 Foreword Welcome to EMBL-EBI’s 2013 Annual Scientific Report. Here we look back on our major achievements during the year, reflecting on the delivery of our world-class services, research, training, industry collaboration and European coordination of life-science data. The past year has been one full of exciting changes, both scientifically and organisationally. We unveiled a new website that helps users explore our resources more seamlessly, saw the publication of ground-breaking work in data storage and synthetic biology, joined the global alliance for global health, built important new relationships with our partners in industry and celebrated the launch of ELIXIR. -
A Unicellular Relative of Animals Generates a Layer of Polarized Cells
RESEARCH ARTICLE A unicellular relative of animals generates a layer of polarized cells by actomyosin- dependent cellularization Omaya Dudin1†*, Andrej Ondracka1†, Xavier Grau-Bove´ 1,2, Arthur AB Haraldsen3, Atsushi Toyoda4, Hiroshi Suga5, Jon Bra˚ te3, In˜ aki Ruiz-Trillo1,6,7* 1Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; 2Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; 3Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway; 4Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; 5Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan; 6Departament de Gene`tica, Microbiologia i Estadı´stica, Universitat de Barcelona, Barcelona, Spain; 7ICREA, Barcelona, Spain Abstract In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an *For correspondence: actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a [email protected] (OD); polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly [email protected] (IR-T) regulated transcriptional activation of genes involved in cell adhesion. -
Global Cellular Response to Chemotherapy- Induced
RESEARCH ARTICLE elife.elifesciences.org Global cellular response to chemotherapy- induced apoptosis Arun P Wiita1,2, Etay Ziv3,4, Paul J Wiita5, Anatoly Urisman1,6, Olivier Julien1, Alma L Burlingame1, Jonathan S Weissman3,7, James A Wells1,3* 1Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States; 2Department of Laboratory Medicine, University of California, San Francisco, San Francisco, United States; 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; 4Department of Radiology, University of California, San Francisco, San Francisco, United States; 5Department of Physics, The College of New Jersey, Ewing, United States; 6Department of Pathology, University of California, San Francisco, San Francisco, United States; 7Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States Abstract How cancer cells globally struggle with a chemotherapeutic insult before succumbing to apoptosis is largely unknown. Here we use an integrated systems-level examination of transcription, translation, and proteolysis to understand these events central to cancer treatment. As a model we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line therapy. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. Simultaneous ribosome profiling further reveals potential translational regulation of stress response genes. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of upstream bortezomib effects. Moreover, previously uncharacterized non-caspase proteolytic events also participate in cellular deconstruction. Our systems-level data also support co-targeting the anti-apoptotic regulator HSF1 to promote cell death by bortezomib. -
Jéssica Michelle Da Silveira Dalsuco
2º CICLO MESTRADO EM FISIOPATOLOGIA CARDIOVASCULAR PERFIL DA EXPRESSÃO PROTEICA NA DOENÇA ARTERIAL CORONÁRIA E FATORES DE RISCO QUANDO ASSOCIADA À ESTENOSE AÓRTICA JÉSSICA MICHELLE DA SILVEIRA DALSUCO M 2019 ORIENTADOR: PROF. DR. ANTÓNIO DE SOUSA BARROS COORIENTADOR: PROF. DR. RUI MIGUEL PINHEIRO VITORINO 2 "Há verdadeiramente duas coisas diferentes: saber e crer que se sabe. A ciência consiste em saber, em crer que se sabe reside a ignorância" Hipócrates 3 4 Agradecimentos Ao Professor Doutor Adelino Leite Moreira, Coordenador do Mestrado em Fisiopatologia Cardiovascular e Diretor do Departamento de Cirurgia e Fisiologia do Centro de Investigação Médica da Faculdade de Medicina da Universidade do Porto, pela oportunidade que me foi concedida em ingressar neste mestrado e na realização desta dissertação. Ao meu orientador, Professor Doutor António Barros e, coorientador, Professor Doutor Rui Vitorino, pelo acompanhamento, disponibilidade, ensinamentos e apoio moral durante a realização da presente dissertação. À Professora Doutora Rita Ferreira pela disponibilidade no auxílio da parte experimental. À Doutora Francisca Saraiva e a sua equipe, pela paciência e apoio incondicional, desde o meu ingresso no mestrado até a realização da dissertação. Aos meus pais, Nasser e Sónia, a minha irmã, Yara e avó Rosa, a quem eu homenageio esta dissertação pois apesar da distância, mantiveram-se sempre presentes com o seu amor, carinho e motivação incondicional. Ao meu namorado, Míchel Tamele, pelo companheirismo, paciência, moral e todo o amor concedido durante estes anos. As minhas amigas, Jéssica Marina, Jéssica Paloma, Patrícia e Lousane, que sempre fizeram questão de estar presente em todas as fases, mesmo longe, e deram me forças para chegar até aqui. -
Strategic Plan 2011-2016
Strategic Plan 2011-2016 Wellcome Trust Sanger Institute Strategic Plan 2011-2016 Mission The Wellcome Trust Sanger Institute uses genome sequences to advance understanding of the biology of humans and pathogens in order to improve human health. -i- Wellcome Trust Sanger Institute Strategic Plan 2011-2016 - ii - Wellcome Trust Sanger Institute Strategic Plan 2011-2016 CONTENTS Foreword ....................................................................................................................................1 Overview .....................................................................................................................................2 1. History and philosophy ............................................................................................................ 5 2. Organisation of the science ..................................................................................................... 5 3. Developments in the scientific portfolio ................................................................................... 7 4. Summary of the Scientific Programmes 2011 – 2016 .............................................................. 8 4.1 Cancer Genetics and Genomics ................................................................................ 8 4.2 Human Genetics ...................................................................................................... 10 4.3 Pathogen Variation .................................................................................................. 13 4.4 Malaria -
The Pfam Protein Families Database Marco Punta1,*, Penny C
D290–D301 Nucleic Acids Research, 2012, Vol. 40, Database issue Published online 29 November 2011 doi:10.1093/nar/gkr1065 The Pfam protein families database Marco Punta1,*, Penny C. Coggill1, Ruth Y. Eberhardt1, Jaina Mistry1, John Tate1, Chris Boursnell1, Ningze Pang1, Kristoffer Forslund2, Goran Ceric3, Jody Clements3, Andreas Heger4, Liisa Holm5, Erik L. L. Sonnhammer2, Sean R. Eddy3, Alex Bateman1 and Robert D. Finn3 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, 2Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden, 3HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA, 4Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3QX, UK and 5Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 Downloaded from (Viikinkaari 5), 00014 Helsinki, Finland Received October 7, 2011; Revised October 26, 2011; Accepted October 27, 2011 http://nar.oxfordjournals.org/ ABSTRACT INTRODUCTION Pfam is a widely used database of protein families, Pfam is a database of protein families, where families are currently containing more than 13 000 manually sets of protein regions that share a significant degree of curated protein families as of release 26.0. Pfam is sequence similarity, thereby suggesting homology. available via servers in the UK (http://pfam.sanger Similarity is detected using the HMMER3 (http:// hmmer.janelia.org/) suite of programs. .ac.uk/), the USA (http://pfam.janelia.org/) and Pfam contains two types of families: high quality, Sweden (http://pfam.sbc.su.se/). -
Análise De Padrões De Interação Entre Serino Proteases E Seus Inibidores Protéicos
UNIVERSIDADE FEDERAL DE MINAS GERAIS INSTITUTO DE CIÊNCIAS BIOLÓGICAS PROGRAMA DE PÓS-GRADUAÇÃO EM BIOINFORMÁTICA ANÁLISE DE PADRÕES DE INTERAÇÃO ENTRE SERINO PROTEASES E SEUS INIBIDORES PROTÉICOS Tese apresentada ao Curso de Pós- graduação em Bioinformática da Universidade Federal de Minas Gerais como requisito parcial para a obtenção do grau de Doutor em Bioinformática. CRISTINA RIBEIRO Orientador: Marcelo Matos Santoro Co-Orientador: Goran Neshich Belo Horizonte 08 de abril de 2009 UNIVERSIDADE FEDERAL DE MINAS GERAIS Folha de Aprovação Análise de Padrões de Interação entre Serino Proteases e seus Inibidores Protéicos CRISTINA RIBEIRO Tese defendida e aprovada pela banca examinadora constituída por Prof. Ph. D. MARCELO MATOS SANTORO – Orientador Universidade Federal de Minas Gerais Ph. D. GORAN NESHICH – Co-Orientador Empresa Brasileira de Pesquisa Agropecuária Prof. Ph. D. MONIQUE ARAÚJO DE BRITO Universidade Federal Fluminense Prof. Ph. D. CAIO JÚLIO MARTINS VELOSO Pontifícia Universidade Católica de Minas Gerais Prof. Ph. D. RONALDO ALVES PINTO NAGEM Universidade Federal de Minas Gerais Ph. D. HUMBERTO D’MUNIZ PEREIRA Universidade de São Paulo Belo Horizonte 08 de abril de 2009 ii “Matar o sonho é matarmo-nos. É mutilar a nossa alma. O sonho é o que temos de realmente nosso, de impenetravelmente e inexpugnavelmente nosso” Fernando Pessoa iii Agradecimentos A Deus, pela vida. Aos meus pais simplesmente por tudo não há como citar ou descrever o que fizeram por mim ao longo desses 30 anos. Agradeço ao Guilherme, pelo carinho e apoio incondicional para que eu fizesse esse doutorado, que tornou a minha vida mais leve e radiante. A você um beijo bom.