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1

Origins of the Loss of Concertedness in Pericyclic Reactions: Theoretical Prediction and Direct Observation of Stepwise Mechanisms in [3 + 2] Thermal Cycloadditions

Vivanco, Silvia, Lecea, Begoña, Arrieta, Ana, Prieto, Pilar, Morao, Iñaki, Linden, Anthony, Cossío, Fernando P.

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 398 KB

english, 2000

2

Determination of syn/anti Isomerism in DCNQI Derivatives by 2D Exchange Spectroscopy: Theoretical Underpinning

Fernando P. Cossío, Pilar de la Cruz, Antonio de la Hoz, Fernando Langa, Nazario Martín, Pilar Prieto, Luis Sánchez

Journal:

European Journal of Organic Chemistry

Year:

2000

Language:

english

File:

PDF, 345 KB

english, 2000

3

ChemInform Abstract: Synthesis of Pyrazolo[3,4-b]pyridines by Cycloaddition Reactions under Microwave Irradiation.

Angel Diaz-Ortiz, Jose Ramon Carrillo, Fernando P. Cossio, Maria J. Gomez-Escalonilla, Antonio de la Hoz, Andres Moreno, Pilar Prieto

Journal:

Year:

2000

File:

PDF, 32 KB

2000

4

ChemInform Abstract: Modification of Regioselectivity in Cycloadditions to C70 under Microwave Irradiation.

Fernando Langa, Pilar de la Cruz, Antonio de la Hoz, Eva Espildora, Fernando P. Cossio, Begona Lecea

Journal:

Year:

2000

File:

PDF, 27 KB

2000

5

Fluorescence detection by intensity changes for high-performance thin-layer chromatography separation of lipids using automated multiple development

Vicente L. Cebolla, Carmen Jarne, Pilar Domingo, Andrés Domínguez, Aránzazu Delgado-Camón, Rosa Garriga, Javier Galbán, Luis Membrado, Eva M. Gálvez, Fernando P. Cossío

Journal:

Journal of Chromatography A

Year:

2011

Language:

english

File:

PDF, 723 KB

english, 2011

6

Selectivity under microwave irradiation. Benzylation of 2-pyridone: an experimental and theoretical study

Antonio de la Hoz, María Pilar Prieto, Michel Rajzmann, Abel de Cózar, Angel Díaz-Ortiz, Andrés Moreno, Fernando P. Cossío

Journal:

Year:

2008

Language:

english

File:

PDF, 664 KB

english, 2008

7

Microwave-assisted reactions of nitroheterocycles with dienes. Diels–Alder and tandem hetero Diels–Alder/[3,3] sigmatropic shift

M. Victoria Gómez, Ana I. Aranda, Andrés Moreno, Fernando P. Cossío, Abel de Cózar, Ángel Díaz-Ortiz, Antonio de la Hoz, Pilar Prieto

Journal:

Year:

2009

Language:

english

File:

PDF, 429 KB

english, 2009

8

Enhancing stereochemical diversity by means of microwave irradiation in the absence of solvent: Synthesis of highly substituted nitroproline esters via 1,3-dipolar reactions

Angel Díaz-Ortiz, Antonio de la Hoz, M. Antonia Herrero, Pilar Prieto, Ana Sánchez-Migallón, Fernando P. Cossío, Ana Arrieta, Silvia Vivanco, Concepción Foces-Foces

Journal:

Molecular Diversity

Year:

2003

Language:

english

File:

PDF, 85 KB

english, 2003

9

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

Cossio, Pilar, Laio, Alessandro, Pietrucci, Fabio

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.68 MB

english, 2011

10

Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations

Giulia Rossetti, Pilar Cossio, Alessandro Laio, Paolo Carloni

Journal:

Year:

2011

Language:

english

File:

PDF, 582 KB

english, 2011

11

Solvent-Free Thermal and Microwave-Assisted [3 + 2] Cycloadditions between Stabilized Azomethine Ylides and Nitrostyrenes. An Experimental and Theoretical Study

Arrieta, Ana, Otaegui, Dorleta, Zubia, Aizpea, Cossío, Fernando P., Díaz-Ortiz, Angel, de la Hoz, Antonio, Herrero, M. Antonia, Prieto, Pilar, Foces-Foces, Concepción, Pizarro, José L., Arriortua, Mar

Journal:

Journal of Organic Chemistry

Year:

2007

Language:

english

File:

PDF, 568 KB

english, 2007

12

Ameloblastic carcinoma of the maxilla: a report of 3 cases

Pedro Infante-Cossio, Jose M. Hernandez-Guisado, Pilar Fernandez-Machin, Alvaro Garcia-Perla, Angel Rollon-Mayordomo, Jose L. Gutierrez-Perez

Journal:

Journal of Cranio-Maxillofacial Surgery

Year:

1998

Language:

english

File:

PDF, 2.58 MB

english, 1998

13

Médicos residentes e industria farmacéutica

Pilar Martín-Aranda, Itziar Vázquez, Ángela Rodríguez de Cossío

Journal:

Atención Primaria

Year:

2007

File:

PDF, 89 KB

2007

14

Modification of Regioselectivity in Cycloadditions to C 70 under Microwave Irradiation

Langa, Fernando, de la Cruz, Pilar, de la Hoz, Antonio, Espíldora, Eva, Cossío, Fernando P., Lecea, Begoña

Journal:

Journal of Organic Chemistry

Year:

2000

Language:

english

File:

PDF, 574 KB

english, 2000

15

Exploring by Enhanced Sampling Techniques: The Protein’s Conformational Space Beyond the PDB

Tejada, Pilar Cossio, Trovato, Antonio, Seno, Flavio, Pietrucci, Fabio, Maritan, Amos, Laio, Alessandro

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 91 KB

english, 2011

16

Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies

Cossio, Pilar, Hummer, Gerhard

Journal:

Journal of Structural Biology

Year:

2013

Language:

english

File:

PDF, 2.13 MB

english, 2013

17

On the Mechanism of Conversion of N- Acyl-4-acyloxy-β-lactams into 2-Substituted 1,3-Oxazin-6-ones. Can a Low-Barrier Transition State Be Antiaromatic?

Alajarín, Mateo, Sánchez-Andrada, Pilar, Cossío, Fernando P., Arrieta, Ana, Lecea, Begoña

Journal:

Journal of Organic Chemistry

Year:

2001

Language:

english

File:

PDF, 187 KB

english, 2001

18

Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model

Cossio, Pilar, Marinelli, Fabrizio, Laio, Alessandro, Pietrucci, Fabio

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 577 KB

english, 2010

19

Effects of a disulfide bridge prior to amyloid formation of the ABRI peptide

Ceballos, Jorge A., Giraldo, Marco A., Cossio, Pilar

Journal:

Year:

2014

Language:

english

File:

PDF, 1.96 MB

english, 2014

20

Theoretical study on the reaction between 4,6-dimethyl-1,2,3-triazine and enamines

Prieto, Pilar, Cossío, Fernando P., Carrillo, José Ramón, Hoz, Antonio de la, Díaz-Ortiz, Ángel, Moreno, Andrés

Journal:

Journal of the Chemical Society Perkin Transactions 2

Year:

2002

Language:

english

File:

PDF, 291 KB

english, 2002

21

Assembling the Pieces of Protein Puzzles

Hummer, Gerhard, Cossio, Pilar, Bahrami, Amir, Jost López, Alfredo, Köfinger, Jürgen

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 35 KB

english, 2015

22

The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin

Grigoriu, Simina, Bond, Rachel, Cossio, Pilar, Chen, Jennifer A., Ly, Nina, Hummer, Gerhard, Page, Rebecca, Cyert, Martha S., Peti, Wolfgang, Petsko, Gregory A.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.15 MB

english, 2013

23

Exploring the Universe of Protein Structures beyond the Protein Data Bank

Cossio, Pilar, Trovato, Antonio, Pietrucci, Fabio, Seno, Flavio, Maritan, Amos, Laio, Alessandro, Lai, Luhua

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.28 MB

english, 2010

24

On artifacts in single-molecule force spectroscopy

Cossio, Pilar, Hummer, Gerhard, Szabo, Attila

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.10 MB

english, 2015

25

On Artifacts in Single-Molecule Force Spectroscopy

Cossio, Pilar, Hummer, Gerhard, Szabo, Attila

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 41 KB

english, 2016

26

Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy

Cossio, Pilar, Hummer, Gerhard, Szabo, Attila

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 1.25 MB

english, 2016

27

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images

Cossio, Pilar, Rohr, David, Baruffa, Fabio, Rampp, Markus, Lindenstruth, Volker, Hummer, Gerhard

Journal:

Computer Physics Communications

Year:

2016

Language:

english

File:

PDF, 2.11 MB

english, 2016

28

A simple and efficient statistical potential for scoring ensembles of protein structures

Cossio, Pilar, Granata, Daniele, Laio, Alessandro, Seno, Flavio, Trovato, Antonio

Journal:

Scientific Reports

Year:

2012

Language:

english

File:

PDF, 440 KB

english, 2012

29

Discovery of antimicrobial compounds targeting bacterial type FAD synthetases

Sebastián, María, Anoz-Carbonell, Ernesto, Gracia, Begoña, Cossio, Pilar, Aínsa, José Antonio, Lans, Isaías, Medina, Milagros

Journal:

Journal of Enzyme Inhibition and Medicinal Chemistry

Year:

2018

Language:

english

File:

PDF, 2.32 MB

english, 2018

30

Transition paths in single-molecule force spectroscopy

Cossio, Pilar, Hummer, Gerhard, Szabo, Attila

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.98 MB

english, 2018

31

Likelihood-based structural analysis of electron microscopy images

Cossio, Pilar, Hummer, Gerhard

Journal:

Current Opinion in Structural Biology

Year:

2018

Language:

english

File:

PDF, 764 KB

english, 2018

32

Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase

Cossio, Pilar, Allegretti, Matteo, Mayer, Florian, Müller, Volker, Vonck, Janet, Hummer, Gerhard

Journal:

Year:

2018

Language:

english

File:

PDF, 474 KB

english, 2018

33

The Dimer-of-Trimers Assembly Prevents Catalysis at the Transferase Site of Prokaryotic FAD Synthase

Lans, Isaias, Seco, Juan, Serrano, Ana, Burbano, Ricardo, Cossio, Pilar, Daza, Martha C., Medina, Milagros

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 1.15 MB

english, 2018

34

Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations

Baftizadeh, Fahimeh, Cossio, Pilar, Pietrucci, Fabio, Laio, Alessandro

Journal:

Current Physical Chemistry

Year:

2012

Language:

english

File:

PDF, 549 KB

english, 2012

35

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids

Ochoa, Rodrigo, Soler, Miguel A., Laio, Alessandro, Cossio, Pilar

Journal:

Physical Chemistry Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.60 MB

english, 2018

36

Exponential consensus ranking improves the outcome in docking and receptor ensemble docking

Palacio-Rodríguez, Karen, Lans, Isaias, Cavasotto, Claudio N., Cossio, Pilar

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 2.44 MB

english, 2019

37

Predicting the affinity of peptides to MHC class II by scoring molecular dynamics simulations

Ochoa, Rodrigo, Laio, Alessandro, Cossio, Pilar

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 3.41 MB

english, 2019

38

Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors

Covino, Roberto, Woodside, Michael T., Hummer, Gerhard, Szabo, Attila, Cossio, Pilar

Journal:

The Journal of Chemical Physics

Year:

2019

Language:

english

File:

PDF, 2.13 MB

english, 2019

39

Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors

Covino, Roberto, Woodside, Michael T., Hummer, Gerhard, Szabo, Attila, Cossio, Pilar

Journal:

The Journal of Chemical Physics

Year:

2019

File:

PDF, 2.13 MB

2019

40

Computational Design of Peptides Bound to the Major Histocompatibility Complex Class II

Ochoa, Rodrigo, Laio, Alessandro, Cossio, Pilar

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

41

Need for Cross-Validation of Single Particle Cryo-EM

Journal:

Journal of Chemical Information and Modeling

Year:

2020

Language:

english

File:

PDF, 1.57 MB

english, 2020

42

Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles

Lans, Isaias, Palacio-RodrÃguez, Karen, Cavasotto, Claudio N., Cossio, Pilar

Journal:

Journal of Computer-Aided Molecular Design

Year:

2020

File:

PDF, 2.28 MB

2020

43

Validation tests for cryo-EM maps using an independent particle set

Ortiz, Sebastian, Stanisic, Luka, Rodriguez, Boris A, Rampp, Markus, Hummer, Gerhard, Cossio, Pilar

Journal:

Journal of Structural Biology: X

Year:

2020

File:

PDF, 2.48 MB

2020

44

In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target

Lans, Isaias, Anoz-Carbonell, Ernesto, Palacio-RodrÃguez, Karen, AÃnsa, JosÃ© Antonio, Medina, Milagros, Cossio, Pilar, MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 2.13 MB

2020

45

PARCE: Protocol for Amino acid Refinement through Computational Evolution

Ochoa, Rodrigo, Soler, Miguel A., Laio, Alessandro, Cossio, Pilar

Journal:

Computer Physics Communications

Year:

2020

File:

PDF, 3.00 MB

2020