Publications by authors named "Modesto Orozco"

100Publications

DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs.

J Chem Theory Comput 2020 Oct 29;16(10):6598-6608. Epub 2020 Sep 29.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1021/acs.jctc.0c00306DOI Listing
October 2020

Bioactive Conformational Ensemble Server and Database. A Public Framework to Speed Up Drug Discovery.

J Chem Theory Comput 2020 Oct 1;16(10):6586-6597. Epub 2020 Sep 1.

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology (BIST). Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/acs.jctc.0c00305DOI Listing
October 2020

Exploring the Conformational Landscape of Bioactive Small Molecules.

J Chem Theory Comput 2020 Oct 2;16(10):6575-6585. Epub 2020 Sep 2.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1021/acs.jctc.0c00304DOI Listing
October 2020

Molywood: streamlining the design and rendering of molecular movies.

Bioinformatics 2020 Jun 23. Epub 2020 Jun 23.

Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btaa584DOI Listing
June 2020

Colibactin DNA-damage signature indicates mutational impact in colorectal cancer.

Nat Med 2020 07 1;26(7):1063-1069. Epub 2020 Jun 1.

Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.

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http://dx.doi.org/10.1038/s41591-020-0908-2DOI Listing
July 2020

Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.

Nucleic Acids Res 2020 06;48(10):5318-5331

Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.

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http://dx.doi.org/10.1093/nar/gkaa285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261198PMC
June 2020

Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry.

Proc Natl Acad Sci U S A 2020 03 12;117(13):7216-7224. Epub 2020 Mar 12.

Maxwell Centre, Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom;

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http://dx.doi.org/10.1073/pnas.1910044117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7132128PMC
March 2020

A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level.

Nucleic Acids Res 2020 03;48(5):e29

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkaa015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049737PMC
March 2020

Determination of a Structural Ensemble Representing the Dynamics of a G-Quadruplex DNA.

Biochemistry 2020 02 23;59(4):379-388. Epub 2019 Dec 23.

Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.

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http://dx.doi.org/10.1021/acs.biochem.9b00493DOI Listing
February 2020

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.

Nucleic Acids Res 2019 12;47(21):11090-11102

Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkz905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868377PMC
December 2019

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.

Nucleic Acids Res 2019 10;47(18):9511-9523

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/nar/gkz759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765203PMC
October 2019

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition.

J Mol Biol 2019 09 17;431(19):3845-3859. Epub 2019 Jul 17.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.07.021DOI Listing
September 2019

VeriNA3d: an R package for nucleic acids data mining.

Bioinformatics 2019 12;35(24):5334-5336

Computational Biology Node, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology.

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http://dx.doi.org/10.1093/bioinformatics/btz553DOI Listing
December 2019

Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease.

Cell 2019 05;177(4):881-895.e17

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Departament de Bioquímica i Biomedicina Molecular, Facultat de Biología, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193039
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http://dx.doi.org/10.1016/j.cell.2019.04.010DOI Listing
May 2019

Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope.

Proc Natl Acad Sci U S A 2019 05 26;116(20):10009-10018. Epub 2019 Apr 26.

Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain;

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http://dx.doi.org/10.1073/pnas.1821442116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525488PMC
May 2019

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond.

Nucleic Acids Res 2019 05;47(9):4418-4430

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gkz255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511876PMC
May 2019

Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics.

Angew Chem Int Ed Engl 2019 03 14;58(12):3759-3763. Epub 2019 Feb 14.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, Barcelona, 08028, Spain.

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http://dx.doi.org/10.1002/anie.201810922DOI Listing
March 2019

A multifunctional toolkit for target-directed cancer therapy.

Chem Commun (Camb) 2019 Jan;55(6):802-805

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1039/c8cc08823cDOI Listing
January 2019

Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B-based photoreceptor.

J Biol Chem 2018 11 27;293(46):17888-17905. Epub 2018 Sep 27.

the Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100,

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http://dx.doi.org/10.1074/jbc.RA118.004838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240859PMC
November 2018

Allosterism and signal transfer in DNA.

Nucleic Acids Res 2018 09;46(15):7554-7565

Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gky549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125689PMC
September 2018

Protein Flexibility and Synergy of HMG Domains Underlie U-Turn Bending of DNA by TFAM in Solution.

Biophys J 2018 05 13;114(10):2386-2396. Epub 2017 Dec 13.

Structural MitoLab, Department of Structural Biology, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.11.3743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028807PMC
May 2018

Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH.

Mol Cell 2017 Nov;68(4):797-807.e7

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.10.021DOI Listing
November 2017

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH.

J Am Chem Soc 2017 10 27;139(40):13985-13988. Epub 2017 Sep 27.

Instituto de Química Física 'Rocasolano', CSIC , Serrano 119, 28006 Madrid, Spain.

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http://dx.doi.org/10.1021/jacs.7b07383DOI Listing
October 2017

Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs.

J Chem Inf Model 2018 16;57(8):2089-2098. Epub 2017 Aug 16.

Joint BSC-CRG-IRB Research Program in Computational Biology. Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain.

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http://dx.doi.org/10.1021/acs.jcim.7b00178DOI Listing
August 2017

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance.

Proc Natl Acad Sci U S A 2017 08 24;114(32):E6526-E6535. Epub 2017 Jul 24.

Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain;

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http://dx.doi.org/10.1073/pnas.1702971114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559014PMC
August 2017

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry.

ACS Cent Sci 2017 May 26;3(5):454-461. Epub 2017 Apr 26.

INSERM, CNRS, Université de Bordeaux, Acides Nucléiques Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France.

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http://dx.doi.org/10.1021/acscentsci.7b00084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445532PMC
May 2017

Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells.

Chem Commun (Camb) 2017 Mar;53(19):2870-2873

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1039/c6cc10287eDOI Listing
March 2017

Proton Dynamics in Protein Mass Spectrometry.

J Phys Chem Lett 2017 Mar 22;8(6):1105-1112. Epub 2017 Feb 22.

Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany.

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http://dx.doi.org/10.1021/acs.jpclett.7b00127DOI Listing
March 2017

Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.

J Chem Theory Comput 2017 Mar 15;13(3):1454-1461. Epub 2017 Feb 15.

Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/acs.jctc.6b01153DOI Listing
March 2017

How accurate are accurate force-fields for B-DNA?

Nucleic Acids Res 2017 04;45(7):4217-4230

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkw1355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397185PMC
April 2017

The Multiple Roles of Waters in Protein Solvation.

J Phys Chem B 2017 04 20;121(15):3636-3643. Epub 2017 Jan 20.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona, 08028, Spain.

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http://dx.doi.org/10.1021/acs.jpcb.6b09676DOI Listing
April 2017

Small Details Matter: The 2'-Hydroxyl as a Conformational Switch in RNA.

J Am Chem Soc 2016 12 13;138(50):16355-16363. Epub 2016 Dec 13.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , 08028 Barcelona, Spain.

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http://dx.doi.org/10.1021/jacs.6b09471DOI Listing
December 2016

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA.

J Phys Chem Lett 2017 Jan 9;8(1):21-28. Epub 2016 Dec 9.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/acs.jpclett.6b02451DOI Listing
January 2017

Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop.

Structure 2017 01 1;25(1):53-65. Epub 2016 Dec 1.

Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio 48160, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.str.2016.11.003DOI Listing
January 2017

DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.

Nucleic Acids Res 2017 01 29;45(2):951-967. Epub 2016 Nov 29.

Structural MitoLab, Department of Structural Biology, "Maria de Maeztu" Unit of Excellence, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain

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http://dx.doi.org/10.1093/nar/gkw1147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314765PMC
January 2017

Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer.

Cancer Res 2017 01 22;77(2):459-469. Epub 2016 Nov 22.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1158/0008-5472.CAN-16-0097DOI Listing
January 2017

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.

Nat Commun 2016 08 31;7:12575. Epub 2016 Aug 31.

Department of Theoretical Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.

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http://dx.doi.org/10.1038/ncomms12575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013691PMC
August 2016

Challenges of docking in large, flexible and promiscuous binding sites.

Bioorg Med Chem 2016 10 6;24(20):4961-4969. Epub 2016 Aug 6.

Joint BSC-IRB Program in Computational Biology. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain; Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Barcelona 08029, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2016.08.010DOI Listing
October 2016

The Differential Response of Proteins to Macromolecular Crowding.

PLoS Comput Biol 2016 07 29;12(7):e1005040. Epub 2016 Jul 29.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966950PMC
July 2016

Saturation of recognition elements blocks evolution of new tRNA identities.

Sci Adv 2016 Apr 29;2(4):e1501860. Epub 2016 Apr 29.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1126/sciadv.1501860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928997PMC
April 2016

Long-timescale dynamics of the Drew-Dickerson dodecamer.

Nucleic Acids Res 2016 05 15;44(9):4052-66. Epub 2016 Apr 15.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkw264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872116PMC
May 2016

Computational Prediction of HIV-1 Resistance to Protease Inhibitors.

J Chem Inf Model 2016 05 5;56(5):915-23. Epub 2016 May 5.

Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain.

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http://dx.doi.org/10.1021/acs.jcim.5b00667DOI Listing
May 2016

Editorial overview: Theory and simulation.

Curr Opin Struct Biol 2016 Apr 25;37:iv-v. Epub 2016 Mar 25.

Indian Institute of Science, Molecular Biophysics Unit, Bangalore, India. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2016.03.004DOI Listing
April 2016

Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression.

Nucleic Acids Res 2016 05 14;44(9):4354-67. Epub 2016 Mar 14.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkw169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872095PMC
May 2016

Nucleosome architecture throughout the cell cycle.

Sci Rep 2016 Jan 28;6:19729. Epub 2016 Jan 28.

Institute for Research in Biomedicine (IRB Barcelona). Baldiri Reixac 10-12. 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/srep19729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730144PMC
January 2016

Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia.

Hum Mol Genet 2016 Mar 10;25(6):1233-46. Epub 2016 Jan 10.

Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain, Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC), Universidad de Zaragoza, Mariano Esquillor, Edificio I + D, 50018 Zaragoza, Spain, Aragon Institute for Health Research (IIS Aragón), Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain

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http://dx.doi.org/10.1093/hmg/ddw004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764198PMC
March 2016

Multiscale simulation of DNA.

Curr Opin Struct Biol 2016 Apr 19;37:29-45. Epub 2015 Dec 19.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain; Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain; Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2015.11.011DOI Listing
April 2016

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins.

Structure 2016 Jan 10;24(1):116-126. Epub 2015 Dec 10.

Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain; Joint BSC-IRB Research Program in Computational Biology, C/Baldiri Reixac 10, 08028 Barcelona, Spain; Department of Biochemistry and Molecular Biology, University of Barcelona, Av. Diagonal 647, 08028 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.str.2015.10.025DOI Listing
January 2016

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

Nucleic Acids Res 2016 Jan 26;44(D1):D272-8. Epub 2015 Nov 26.

Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkv1301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702913PMC
January 2016

Molecular dynamics simulations: advances and applications.

Adv Appl Bioinform Chem 2015 19;8:37-47. Epub 2015 Nov 19.

Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.2147/AABC.S70333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4655909PMC
November 2015

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

J Chem Theory Comput 2015 Dec 20;11(12):5929-38. Epub 2015 Nov 20.

Institute for Research in Biomedicine (IRB Barcelona) , Baldiri i Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/acs.jctc.5b00660DOI Listing
December 2015

Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties.

Org Lett 2015 Nov 22;17(21):5416-9. Epub 2015 Oct 22.

Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.

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http://dx.doi.org/10.1021/acs.orglett.5b02769DOI Listing
November 2015

SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS.

Sci Rep 2015 Oct 9;5:14809. Epub 2015 Oct 9.

Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1038/srep14809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598734PMC
October 2015

Inntags: small self-structured epitopes for innocuous protein tagging.

Nat Methods 2015 Oct 31;12(10):955-8. Epub 2015 Aug 31.

Molecular Biology Institute of Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.

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http://dx.doi.org/10.1038/nmeth.3556DOI Listing
October 2015

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH.

Angew Chem Int Ed Engl 2015 Sep 24;54(36):10488-91. Epub 2015 Jul 24.

Institute for Research in Biomedicine (IRB Barcelona), Joint BSC-IRB Research Program in Computational Biology, Barcelona (Spain).

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http://dx.doi.org/10.1002/anie.201503770DOI Listing
September 2015

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

J Am Chem Soc 2015 Aug 10;137(32):10205-15. Epub 2015 Aug 10.

‡Joint BSC-CRG-IRB Programme on Computational Biology, Institute for Research in Biomedicine, Baldiri i Reixac 19, 08028, Barcelona, Spain.

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http://pubs.acs.org/doi/10.1021/jacs.5b04086
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http://dx.doi.org/10.1021/jacs.5b04086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251407PMC
August 2015

The structural impact of DNA mismatches.

Nucleic Acids Res 2015 Apr 27;43(8):4309-21. Epub 2015 Mar 27.

Joint BSC-CRG-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain

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http://dx.doi.org/10.1093/nar/gkv254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417165PMC
April 2015

Molecular dynamics study of naturally existing cavity couplings in proteins.

PLoS One 2015 27;10(3):e0119978. Epub 2015 Mar 27.

Translational Bioinformatics in Neurosciences, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119978PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376744PMC
February 2016

Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids.

J Org Chem 2015 Mar 5;80(6):3083-91. Epub 2015 Mar 5.

†Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.

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http://dx.doi.org/10.1021/jo502948tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484724PMC
March 2015

Tribute to William L. Jorgensen.

J Phys Chem B 2015 Jan;119(3):621-3

University of Minnesota and Jilin University.

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http://dx.doi.org/10.1021/jp511519wDOI Listing
January 2015

Visualizing phosphodiester-bond hydrolysis by an endonuclease.

Nat Struct Mol Biol 2015 Jan 8;22(1):65-72. Epub 2014 Dec 8.

1] Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [2] Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/nsmb.2932DOI Listing
January 2015

Structure and dynamics of oligonucleotides in the gas phase.

Angew Chem Int Ed Engl 2015 Jan 21;54(2):467-71. Epub 2014 Nov 21.

Institute for Research in Biomedicine (IRB Barcelona), Joint BSC-CRG-IRB Program on Computational Biology, Barcelona (Spain).

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http://mmb.pcb.ub.es/~gportella/pdf/Arcella_Angew_2015.pdf
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http://doi.wiley.com/10.1002/anie.201406910
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http://dx.doi.org/10.1002/anie.201406910DOI Listing
January 2015

SEABED: Small molEcule activity scanner weB servicE baseD.

Bioinformatics 2015 Mar 27;31(5):773-5. Epub 2014 Oct 27.

Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain, Joint BSC-CRG-IRB Program in Computational Biology, Barcelona, Spain, Computational Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08034, Spain, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Department of Biochemistry and Molecular Biology, Biology Faculty, University of Barcelona, Barcelona 08028, Spain and Structural Bioinformatics Node, National Institute of Bioinformatics, Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btu709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7297214PMC
March 2015

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

Nat Biotechnol 2014 Nov 26;32(11):1106-12. Epub 2014 Oct 26.

1] Joint IRB-BSC Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain. [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1038/nbt.3027DOI Listing
November 2014

Assessing the suitability of the multilevel strategy for the conformational analysis of small ligands.

J Phys Chem B 2015 Jan 29;119(3):1164-72. Epub 2014 Oct 29.

Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona , Avda. Prat de la Riba, 171, 08921 Santa Coloma de Gramenet, Spain.

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http://dx.doi.org/10.1021/jp506779yDOI Listing
January 2015

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA.

Nucleic Acids Res 2014 Oct 15;42(18):11304-20. Epub 2014 Sep 15.

Joint BSC-CRG-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain Departament de Bioquimica, Facultat de Biologia, Avgda Diagonal 647, Barcelona 08028, Spain

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http://dx.doi.org/10.1093/nar/gku809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191396PMC
October 2014

Direct measurement of the dielectric polarization properties of DNA.

Proc Natl Acad Sci U S A 2014 Sep 18;111(35):E3624-30. Epub 2014 Aug 18.

Institut de Bioenginyeria de Catalunya, 08028 Barcelona, Spain; and Departament d'Electrònica, Universitat de Barcelona, 08028 Barcelona, Spain

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http://dx.doi.org/10.1073/pnas.1405702111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156767PMC
September 2014

A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition.

Cancer Res 2014 Oct 8;74(19):5608-19. Epub 2014 Aug 8.

Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-3659DOI Listing
October 2014

Structure and properties of DNA in apolar solvents.

J Phys Chem B 2014 Jul 14;118(29):8540-8. Epub 2014 Jul 14.

Institute for Research in Biomedicine (IRB Barcelona) , 08028 Barcelona, Spain.

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http://dx.doi.org/10.1021/jp503816rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124876PMC
July 2014

Correlated motions are a fundamental property of β-sheets.

Nat Commun 2014 Jun 11;5:4070. Epub 2014 Jun 11.

1] Joint BSC-CRG-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms5070DOI Listing
June 2014

A theoretical view of protein dynamics.

Authors:
Modesto Orozco

Chem Soc Rev 2014 Jul 8;43(14):5051-66. Epub 2014 Apr 8.

Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain.

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http://dx.doi.org/10.1039/c3cs60474hDOI Listing
July 2014

Fuzziness and noise in nucleosomal architecture.

Nucleic Acids Res 2014 Apr 27;42(8):4934-46. Epub 2014 Feb 27.

Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain and Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gku165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005669PMC
April 2014

MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents.

J Am Chem Soc 2014 Feb 14;136(8):3075-86. Epub 2014 Feb 14.

Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine , Josep Samitier 1-5 and Barcelona Supercomputing Center, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/ja410698uDOI Listing
February 2014

Exploring early stages of the chemical unfolding of proteins at the proteome scale.

PLoS Comput Biol 2013 12;9(12):e1003393. Epub 2013 Dec 12.

Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain ; Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1003393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861036PMC
August 2014

BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

BMC Struct Biol 2013 Dec 13;13:32. Epub 2013 Dec 13.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1186/1472-6807-13-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924234PMC
December 2013

Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures.

FEBS J 2014 Feb 2;281(4):1085-99. Epub 2014 Jan 2.

Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain.

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http://dx.doi.org/10.1111/febs.12670DOI Listing
February 2014

The DNA-forming properties of 6-selenoguanine.

Phys Chem Chem Phys 2014 Jan 28;16(3):1101-10. Epub 2013 Nov 28.

Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1039/c3cp53885kDOI Listing
January 2014

Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

PLoS Comput Biol 2013 21;9(11):e1003354. Epub 2013 Nov 21.

Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain ; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1003354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836855PMC
July 2014

The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator.

J Phys Chem B 2013 Nov 28;117(44):13842-50. Epub 2013 Oct 28.

Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600036, India.

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http://dx.doi.org/10.1021/jp408350vDOI Listing
November 2013

Backbone FC-H···O hydrogen bonds in 2'F-substituted nucleic acids.

Angew Chem Int Ed Engl 2013 Nov 23;52(46):12065-8. Epub 2013 Sep 23.

Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid (Spain).

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http://dx.doi.org/10.1002/anie.201305710DOI Listing
November 2013

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.

J Chem Theory Comput 2013 ;9(1):707-721

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic ; Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic.

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http://dx.doi.org/10.1021/ct300671yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748671PMC
January 2013

On the nature of DNA hyperchromic effect.

J Phys Chem B 2013 Jul 12;117(29):8697-704. Epub 2013 Jul 12.

CINECA - Roma, via dei Tizii, 6, 00185, Roma, Italy.

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http://dx.doi.org/10.1021/jp403369kDOI Listing
July 2013