Electronic and Atomic Protein Modeling (EAPM)

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Mostrando 1 - 30 resultados de 183

2025

Laccase and Polyphenol OxidaseIn silico bioprospecting and engineering laccases: Methods and applications

R. Xiang, M. Floor, L. H. Østergaard, K. M. Schnorr, and V. Guallar

2024

Exploiting cyclodextrins as artificial chaperones to enhance enzyme protection through supramolecular engineering

Nanoscale

A. ForoutanKalourazi, S. Amirabbas Nazemi, A. Roshan Unn Parambil, R. Muñoz-Tafalla, P. Vidal, S. S. Shahangian, V. Guallar, M. Ferrer, and P. Shahgaldian
Behind the Scenes of PluriZyme Designs

Eng

A. Robles-Martín, S. Roda, R. Muñoz-Tafalla, and V. Guallar
Multi-scale signaling and tumor evolution in high-grade gliomas

Cancer Cell

J. Liu, S. Cao, K. J. Imbach, M. A. Gritsenko, T-S. M. Lih, J. E. Kyle, T. M. Yaron-Barir, Z. A. Binder, Y. Li, I. Strunilin, et al.
Discovery and biochemical characterization of thermostable glycerol oxidases

Applied Microbiology and Biotechnology

L. L. Santema, L. Rotilio, R. Xiang, G. Tjallinks, V. Guallar, A. Mattevi, and M. W. Fraaije
Immunisation efficacy of a stabilised SARS-CoV-2 spike glycoprotein in two geriatric animal models

npj Vaccines

C. Usai, E. Ainsua-Enrich, V. Urrea Gales, E. Pradenas, C. Lorca-Oró, F. Tarrés-Freixas, N. Roca, M. Pérez, C. Ávila-Nieto, M. Luisa Rodr de la Concepción, N. Pedreño-Lopez, J. Carabelli, B. Trinité, E. Ballana, E. Riveira-Muñoz, N. Izquierdo-Useros, B. Clotet, J. Blanco, V. Guallar, G. Cantero, J. Vergara-Alert, J. Carrillo, and J. Segalés
Structure and mechanisms of transport of human Asc1/CD98hc amino acid transporter

Nature Communications

J. Rullo-Tubau, M. Martinez-Molledo, P. Bartoccioni, I. Puch-Giner, Á. Arias, S. Saen-oon, C. Stephan- Ot Attolini, R. Artuch, L. Díaz, V. Guallar, E. Errasti-Murugarren, M. Palacín, and O. Llorca
Unlocking a Key Residue in a Lipase for Efficient Polyethylene Terephthalate (PET) Hydrolysis and Influencing Depolymerization Product Profiles

ChemCatChem

P. Vidal, A. Robles‐Martín, L. Fernandez‐Lopez, J. L. Gonzalez‐Alfonso, D. Almendral, R. Muñoz‐Tafalla, F. J. Plou, V. Guallar, and M. Ferrer
Immunization with V987H-stabilized Spike glycoprotein protects K18-hACE2 mice and golden Syrian hamsters upon SARS-CoV-2 infection

Nature Communications

C. Ávila-Nieto, J. Vergara-Alert, P. Amengual-Rigo, E. Ainsua-Enrich, M. Brustolin, M. Luisa Rodr de la Concepción, N. Pedreño-Lopez, J. Rodon, V. Urrea, E. Pradenas, S. Marfil, E. Ballana, E. Riveira-Muñoz, M. Pérez, N. Roca, F. Tarrés-Freixas, G. Cantero, A. Pons-Grífols, C. Rovirosa, C. Aguilar-Gurrieri, R. Ortiz, A. Barajas, B. Trinité, R. Lepore, J. Muñoz-Basagoiti, D. Perez-Zsolt, N. Izquierdo-Useros, A. Valencia, J. Blanco, V. Guallar, B. Clotet, J. Segalés, and J. Carrillo
Virus-like particle-mediated delivery of structure-selected neoantigens demonstrates immunogenicity and antitumoral activity in mice

Journal of Translational Medicine

A. Barajas, P. Amengual-Rigo, A. Pons-Grífols, R. Ortiz, O. Gracia Carmona, V. Urrea, N. de la Iglesia, J. Blanco-Heredia, C. Anjos-Souza, I. Varela, B. Trinité, F. Tarrés-Freixas, C. Rovirosa, R. Lepore, M. Vazquez, L. De Mattos-Arruda, A. Valencia, B. Clotet, C. Aguilar-Gurrieri, V. Guallar, J. Carrillo, and J. Blanco

2023

Methods in Molecular BiologyComputational Vaccine DesignNetCleave: An Open-Source Algorithm for Predicting C-Terminal Antigen Processing for MHC-I and MHC-II

R. Farriol-Duran, M. Vallejo-Vallés, P. Amengual-Rigo, M. Floor, and V. Guallar
Enzymes for consumer products to achieve climate neutrality

Oxford Open Climate Change

P. Molina-Espeja, J. Sanz-Aparicio, P. N. Golyshin, A. Robles-Martín, V. Guallar, F. Beltrametti, M. Müller, M. M. Yakimov, J. Modregger, M. van Logchem, P. Corvini, P. Shahgaldian, C. Degering, S. Wieland, A. Timm, C. C. C. R. de Carvalho, I. Re, S. Daniotti, S. Thies, K-E. Jaeger, J. Chow, W. R. Streit, R. Lottenbach, R. Rösch, N. Ansari, and M. Ferrer
Sub-micro- and nano-sized polyethylene terephthalate deconstruction with engineered protein nanopores

Nature Catalysis

A. Robles-Martín, R. Amigot-Sánchez, L. Fernandez-Lopez, J. L. Gonzalez-Alfonso, S. Roda, V. Alcolea-Rodriguez, D. Heras-Márquez, D. Almendral, C. Coscolín, F. J. Plou, R. Portela, M. A. Bañares, Á. Martínez-del-Pozo, S. García-Linares, M. Ferrer, and V. Guallar
Rational engineering of AA5_2 copper radical oxidases to probe the molecular determinants governing their substrate selectivity

The FEBS Journal

R. Koncitikova, L. Zuily, E. Lemarié, D. Ribeaucourt, S. Saker, M. Haon, H. Brumer, V. Guallar, J‐G. Berrin, and M. Lafond
Selective inhibitors of the PSEN1–gamma-secretase complex

Journal of Biological Chemistry

L. Serneels, R. Narlawar, L. Perez-Benito, M. Municoy, V. Guallar, D. T’Syen, M. Dewilde, F. Bischoff, E. Fraiponts, G. Tresadern, P. W. M. Roevens, H. J. M. Gijsen, and B. De Strooper
Peroxygenase‐Catalysed Selective Oxidation of Silanes to Silanols

Angewandte Chemie International Edition

X. Xu, J. M. A. van Hengst, Y. Mao, M. Martinez, S. Roda, M. Floor, V. Guallar, C. E. Paul, M. Alcalde, and F. Hollmann
Combining machine‐learning and molecular‐modeling methods for drug‐target affinity predictions

WIREs Computational Molecular Science

C. Perez‐Lopez, A. Molina, E. Lozoya, V. Segarra, M. Municoy, and V. Guallar
Enhancing the Hydrolytic Activity of a Lipase towards Larger Triglycerides through Lid Domain Engineering

International Journal of Molecular Sciences

L. Fernandez-Lopez, S. Roda, A. Robles-Martín, R. Muñoz-Tafalla, D. Almendral, M. Ferrer, and V. Guallar
Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs

Scientific Reports

J-L. Reyre, S. Grisel, M. Haon, R. Xiang, J-C. Gaillard, J. Armengaud, V. Guallar, A. Margeot, S. Arragain, J-G. Berrin, and B. Bissaro
Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures

Journal of Chemical Information and Modeling

A. M. Díaz-Rovira, H. Martín, T. Beuming, L. Díaz, V. Guallar, and S. S. Ray
AsiteDesign: a Semirational Algorithm for an Automated Enzyme DesignAsiteDesign: a Semirational Algorithm for an Automated Enzyme Design

The Journal of Physical Chemistry B

S. Roda, H. Terholsen, J. Ruth Heike Meyer, A. Cañellas-Solé, V. Guallar, U. Bornscheuer, and M. Kazemi

2022

A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions

Angewandte Chemie International Edition

S. Roda, L. Fernandez‐Lopez, M. Benedens, A. Bollinger, S. Thies, J. Schumacher, C. Coscolín, M. Kazemi, G. Santiago, C. G. W. Gertzen, J. L. Gonzalez‐Alfonso, F. J. Plou, K‐E. Jaeger, S. H. J. Smits, M. Ferrer, and V. Guallar
EP-Pred: A Machine Learning Tool for Bioprospecting Promiscuous Ester Hydrolases

Biomolecules

R. Xiang, L. Fernandez-Lopez, A. Robles-Martín, M. Ferrer, and V. Guallar
Design and Characterization of In-One Protease-Esterase PluriZyme

International Journal of Molecular Sciences

L. Fernandez-Lopez, S. Roda, J. L. Gonzalez-Alfonso, F. J. Plou, V. Guallar, and M. Ferrer
Recent PELE Developments and Applications in Drug Discovery Campaigns

International Journal of Molecular Sciences

I. Puch-Giner, A. Molina, M. Municoy, C. Perez, and V. Guallar
Tandem metalloenzymes gate plant cell entry by pathogenic fungi

Science Advances

B. Bissaro, S. Kodama, T. Nishiuchi, A. Maria Díaz-Rovira, H. Hage, D. Ribeaucourt, M. Haon, S. Grisel, J. A. Simaan, F. Beisson, S. M. Forget, H. Brumer, M-N. Rosso, V. Guallar, R. O’Connell, M. Lafond, Y. Kubo, and J-G. Berrin
Small molecule interactions with the SARS-CoV-2 main protease: In silico all-atom microsecond MD simulations, PELE Monte Carlo simulations, and determination of in vitro activity inhibition

Journal of Molecular Graphics and Modelling

J. Liang, E. Pitsillou, K. Ververis, V. Guallar, A. Hung, and T. C. Karagiannis
Structural Elucidation and Engineering of a Bacterial Carbohydrate Oxidase

Biochemistry

A. Boverio, W. S. Widodo, L. L. Santema, H. J. Rozeboom, R. Xiang, V. Guallar, A. Mattevi, and M. W. Fraaije
Investigation of small molecule inhibitors of the SARS-CoV-2 papain-like protease by all-atom microsecond modelling, PELE Monte Carlo simulations, and in vitro activity inhibition

Chemical Physics Letters

J. J. Liang, E. Pitsillou, K. Ververis, V. Guallar, A. Hung, and T. C. Karagiannis
Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation

Frontiers in Microbiology

P. Vidal, M. Martínez-Martínez, L. Fernandez-Lopez, S. Roda, C. Méndez-García, O. V. Golyshina, V. Guallar, A. I. Peláez, and M. Ferrer

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