Jose Maria Carazo

Jose Maria Carazo

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Jose Maria Carazo

Jose Maria Carazo

Publications by authors named "Jose Maria Carazo"

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Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data.

Prog Biophys Mol Biol 2020 May 26. Epub 2020 May 26.

Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014, Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental and Sciences, University of Helsinki, 00014, Helsinki, Finland; Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.pbiomolbio.2020.05.004DOI Listing
May 2020

Automatic local resolution-based sharpening of cryo-EM maps.

Bioinformatics 2020 Feb;36(3):765-772

Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Univ. Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz671DOI Listing
February 2020

Measuring local-directional resolution and local anisotropy in cryo-EM maps.

Nat Commun 2020 01 2;11(1):55. Epub 2020 Jan 2.

Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049, Cantoblanco, Madrid, Spain.

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http://dx.doi.org/10.1038/s41467-019-13742-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6940361PMC
January 2020

: a new deep-learning- and aspect-based local resolution method for electron-microscopy maps.

IUCrJ 2019 Nov 18;6(Pt 6):1054-1063. Epub 2019 Sep 18.

Biocomputing Unit, National Center for Biotechnology (CSIC), Calle Darwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1107/S2052252519011692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6830216PMC
November 2019

, a deep learning-based approach for particle pruning in cryo-electron microscopy.

IUCrJ 2018 Nov 30;5(Pt 6):854-865. Epub 2018 Oct 30.

Biocomputing Unit, Spanish National Center for Biotechnology, Calle Darwin 3, 28049 Madrid, Spain.

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http://scripts.iucr.org/cgi-bin/paper?S2052252518014392
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http://dx.doi.org/10.1107/S2052252518014392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211526PMC
November 2018

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.

Structure 2018 02 27;26(2):337-344.e4. Epub 2018 Jan 27.

Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain; Department of Engineering of Electronic and Telecommunication Systems, Universidad San Pablo-CEU, Campus Urbanización Montepríncipe, Boadilla del Monte, 28668 Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.str.2017.12.018DOI Listing
February 2018

3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures.

Molecules 2017 Dec 15;22(12). Epub 2017 Dec 15.

GN7 of the Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, 28049 Madrid, Spain.

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http://dx.doi.org/10.3390/molecules22122230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6149929PMC
December 2017

Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ.

Nat Commun 2016 08 26;7:12524. Epub 2016 Aug 26.

Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.

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http://dx.doi.org/10.1038/ncomms12524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007439PMC
August 2016

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

Biophys J 2016 04;110(8):1753-1765

IMPMC, Sorbonne Universités, CNRS UMR 7590, Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, IRD UMR 206, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2016.03.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850348PMC
April 2016

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

Biophys J 2016 Feb 7;110(4):766-75. Epub 2016 Jan 7.

GN7, Spanish National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)/Instruct Image Processing Center, Madrid, Spain.

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http://dx.doi.org/10.1016/j.bpj.2015.11.3519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775853PMC
February 2016

Alignment of direct detection device micrographs using a robust Optical Flow approach.

J Struct Biol 2015 Mar 12;189(3):163-76. Epub 2015 Feb 12.

Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Madrid, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2015.02.001DOI Listing
March 2015

On the development of three new tools for organizing and sharing information in three-dimensional electron microscopy.

Acta Crystallogr D Biol Crystallogr 2013 May 19;69(Pt 5):695-700. Epub 2013 Apr 19.

Escuela Politécnica Superior, Universidad Autonoma de Madrid, 28049 Madrid, Spain.

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http://dx.doi.org/10.1107/S0907444913007038DOI Listing
May 2013

Integrating human and murine anatomical gene expression data for improved comparisons.

Bioinformatics 2012 Feb 20;28(3):397-402. Epub 2011 Nov 20.

GN7 of the National Institute for Bioinformatics, Darwin, 3, 28049 Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btr639DOI Listing
February 2012

Maximum likelihood based classification of electron tomographic data.

J Struct Biol 2011 Jan 16;173(1):77-85. Epub 2010 Aug 16.

Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1016/j.jsb.2010.08.005DOI Listing
January 2011

An introduction to maximum-likelihood methods in cryo-EM.

Methods Enzymol 2010 ;482:263-94

Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1016/S0076-6879(10)82011-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051286PMC
January 2011

Dynamic effects of cofactors and DNA on the oligomeric state of human mitochondrial DNA helicase.

J Biol Chem 2010 May 8;285(19):14639-47. Epub 2010 Mar 8.

Department of Biochemistry and Molecular Biology and the Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, Michigan 49924-1319, USA.

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http://dx.doi.org/10.1074/jbc.M109.099663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863210PMC
May 2010

Conformational rearrangements of SV40 large T antigen during early replication events.

J Mol Biol 2010 Apr 26;397(5):1276-86. Epub 2010 Feb 26.

Unidad de Biocomputación, Centro Nacional de Biotecnología-CSIC, C/Darwin 3, 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/j.jmb.2010.02.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862297PMC
April 2010

tmRNA.SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes.

J Struct Biol 2010 Mar 31;169(3):342-8. Epub 2009 Oct 31.

Department of Biosciences and Nutrition, Karolinska Institutet and School of Technology and Health, Royal Institute of Technology, Novum, S-141 57 Huddinge, Sweden.

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http://dx.doi.org/10.1016/j.jsb.2009.10.015DOI Listing
March 2010

Moara: a Java library for extracting and normalizing gene and protein mentions.

BMC Bioinformatics 2010 Mar 26;11:157. Epub 2010 Mar 26.

BioComputing Unit, National Center of Biotechnology (CNB-CSIC), Madrid, Spain.

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http://dx.doi.org/10.1186/1471-2105-11-157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851609PMC
March 2010

aGEM: an integrative system for analyzing spatial-temporal gene-expression information.

Bioinformatics 2009 Oct 9;25(19):2566-72. Epub 2009 Jul 9.

GN7 of the National Institute for Bioinformatics and Biocomputing Unit of the National Centre for Biotechnology, Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btp422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752607PMC
October 2009

SENT: semantic features in text.

Nucleic Acids Res 2009 Jul 20;37(Web Server issue):W153-9. Epub 2009 May 20.

Software Engineering Department, Complutense University and Biocomputing Unit, National Center for Biotechnology, CNB-CSIC, Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkp392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703940PMC
July 2009

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.

Nucleic Acids Res 2009 Jul 22;37(Web Server issue):W317-22. Epub 2009 May 22.

Computer Architecture Department, Complutense University of Madrid, Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkp416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703901PMC
July 2009

Introducing robustness to maximum-likelihood refinement of electron-microscopy data.

Acta Crystallogr D Biol Crystallogr 2009 Jul 20;65(Pt 7):672-8. Epub 2009 Jun 20.

Centro Nacional de Biotecnología-CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.

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http://scripts.iucr.org/cgi-bin/paper?S0907444909012049
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http://dx.doi.org/10.1107/S0907444909012049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703573PMC
July 2009

Maximum likelihood refinement of electron microscopy data with normalization errors.

J Struct Biol 2009 May 21;166(2):234-40. Epub 2009 Feb 21.

Centro Nacional de Biotecnología-CSIC, Calle Darwin 3, Campus Universidad Autonoma, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/j.jsb.2009.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2693001PMC
May 2009

Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra.

BMC Struct Biol 2009 Mar 26;9:18. Epub 2009 Mar 26.

Escuela Politécnica Superior, Universidad San Pablo-CEU, Campus Urb, Montepríncipe s/n, E-28668 Boadilla del Monte, Madrid, Spain.

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http://dx.doi.org/10.1186/1472-6807-9-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683171PMC
March 2009

Comparison of molecular dynamics and superfamily spaces of protein domain deformation.

BMC Struct Biol 2009 Feb 17;9. Epub 2009 Feb 17.

Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain.

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http://dx.doi.org/10.1186/1472-6807-9-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666742PMC
February 2009

CentrosomeDB: a human centrosomal proteins database.

Nucleic Acids Res 2009 Jan 29;37(Database issue):D175-80. Epub 2008 Oct 29.

Computer Architecture Department, Complutense University of Madrid, Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkn815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686521PMC
January 2009

Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase.

Proc Natl Acad Sci U S A 2008 Dec 10;105(51):20191-6. Epub 2008 Dec 10.

Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1073/pnas.0808037105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629282PMC
December 2008

Image processing for electron microscopy single-particle analysis using XMIPP.

Nat Protoc 2008 ;3(6):977-90

Centro Nacional de Biotecnología CSIC, Unidad de Biocomputación, Cantoblanco, 28049 Madrid, Spain.

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http://dx.doi.org/10.1038/nprot.2008.62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778070PMC
September 2008

ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data.

Bioinformatics 2008 May 12;24(9):1208-9. Epub 2008 Mar 12.

BioComputing Unit, National Center of Biotechnology (CSIC), Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btn094DOI Listing
May 2008

Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex.

Proc Natl Acad Sci U S A 2007 Jul 9;104(30):12324-9. Epub 2007 Jul 9.

Medical Research Council Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0705069104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1941468PMC
July 2007

Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase.

J Mol Biol 2007 Mar 9;367(3):764-9. Epub 2007 Jan 9.

Departmento de Estructura de Macromoléculas, Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.

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http://linkinghub.elsevier.com/retrieve/pii/S002228360700013
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http://dx.doi.org/10.1016/j.jmb.2006.12.075DOI Listing
March 2007

Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.

Nat Methods 2007 Jan 10;4(1):27-9. Epub 2006 Dec 10.

Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049, Madrid, Spain.

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http://dx.doi.org/10.1038/nmeth992DOI Listing
January 2007

On the nature of 2D crystal unbending.

J Struct Biol 2006 Dec 4;156(3):546-55. Epub 2006 Aug 4.

Centro Nacional de Biotecnología. Ciudad Universitaria de Cantoblanco, Calle Darwin, 3, 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/j.jsb.2006.07.012DOI Listing
December 2006

Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.

Structure 2006 Jul;14(7):1115-26

Biocomputing Unit, National Center for Biotechnology-CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/j.str.2006.05.013DOI Listing
July 2006

Structural basis for the cooperative assembly of large T antigen on the origin of replication.

J Mol Biol 2006 Apr 26;357(4):1295-305. Epub 2006 Jan 26.

Centro Nacional de Biotecnología, Darwin 3, Cantoblanco 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/j.jmb.2006.01.021DOI Listing
April 2006

Quaternary polymorphism of replicative helicase G40P: structural mapping and domain rearrangement.

J Mol Biol 2006 Apr 9;357(4):1063-76. Epub 2006 Feb 9.

Department of Macro-molecular Structure, Centro Nacional de Biotecnología, CSIC, Campus Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.

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http://dx.doi.org/10.1016/j.jmb.2006.01.091DOI Listing
April 2006

Fast maximum-likelihood refinement of electron microscopy images.

Bioinformatics 2005 Sep;21 Suppl 2:ii243-4

Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti1140DOI Listing
September 2005

Maximum-likelihood multi-reference refinement for electron microscopy images.

J Mol Biol 2005 Apr;348(1):139-49

Biocomputing Unit, Centro Nacional de Biotecnología, Campus Universidad Autónoma, Cantoblanco, 28049, Madrid, Spain.

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http://dx.doi.org/10.1016/j.jmb.2005.02.031DOI Listing
April 2005

SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps.

J Mol Biol 2005 Jan;345(4):759-71

National Center for Biotechnology, Universidad Autónoma de Madrid, 28049 Madrid, Spain.

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http://dx.doi.org/10.1016/j.jmb.2004.11.005DOI Listing
January 2005

High-performance electron tomography of complex biological specimens.

J Struct Biol 2002 Apr-May;138(1-2):6-20

Departamento de Arquitectura de Computadores, Universidad de Almería, 04120 Almería, Spain.

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http://dx.doi.org/10.1016/s1047-8477(02)00017-5DOI Listing
July 2003

Engene: the processing and exploratory analysis of gene expression data.

Bioinformatics 2003 Mar;19(5):657-8

Computer Architecture Department, Universidad de Málaga, 29080 Málaga, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btg028DOI Listing
March 2003

New electron microscopy database and deposition system.

Trends Biochem Sci 2002 Nov;27(11):589

European Bioinformatics Institute, EMBL Outstation Hinxton, Wellcome Trust Genome Campus, Cambridge, UK CB10 1SD.

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http://dx.doi.org/10.1016/s0968-0004(02)02176-xDOI Listing
November 2002