Electronic and Atomic Protein Modeling (EAPM)

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Showing 1 - 30 results of 173

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
Chronological brain lesions after SARS-CoV-2 infection in hACE2-transgenic mice

Veterinary Pathology

E. Vidal, C. López-Figueroa, J. Rodon, M. Pérez, M. Brustolin, G. Cantero, V. Guallar, N. Izquierdo-Useros, J. Carrillo, J. Blanco, B. Clotet, J. Vergara-Alert, and J. Segalés
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
Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures

Journal of Chemical Information and Modeling

T. Beuming, H. Martín, A. M. Díaz-Rovira, L. Díaz, V. Guallar, and S. S. Ray

2021

Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals

Viruses

B. Trinité, E. Pradenas, S. Marfil, C. Rovirosa, V. Urrea, F. Tarrés-Freixas, R. Ortiz, J. Rodon, J. Vergara-Alert, J. Segalés, V. Guallar, R. Lepore, N. Izquierdo-Useros, G. Trujillo, J. Trapé, C. González-Fernández, A. Flor, R. Pérez-Vidal, R. Toledo, A. Chamorro, R. Paredes, I. Blanco, E. Grau, M. Massanella, J. Carrillo, B. Clotet, and J. Blanco
Mapping Potential Determinants of Peroxidative Activity in an Evolved Fungal Peroxygenase from Agrocybe aegerita

Frontiers in Bioengineering and Biotechnology

P. Molina-Espeja, A. Beltran-Nogal, M. Alejandra Alfuzzi, V. Guallar, and M. Alcalde
Mapping Potential Determinants of Peroxidative Activity in an Evolved Fungal Peroxygenase from Agrocybe aegerita

Frontiers in Bioengineering and Biotechnology

P. Molina-Espeja, A. Beltran-Nogal, M. Alejandra Alfuzzi, V. Guallar, and M. Alcalde
Embelin potentiates venetoclax-induced apoptosis in acute myeloid leukemia cells

Toxicology in Vitro

C. Sofia MateReis-Silva, P. Cristina Branco, K. Lima, F. Lima Silva, P. Roberto Hr Moreno, V. Guallar, L. Veras Costa-Lotufo, and J. Agostinho Machado-Neto
Mutations Suppressing the Lack of Prepilin Peptidase Provide Insights Into the Maturation of the Major Pilin Protein in Cyanobacteria

Frontiers in Microbiology

M. Linhartová, P. Skotnicová, K. Hakkila, M. Tichý, J. Komenda, J. Knoppová, J. F. Gilabert, V. Guallar, T. Tyystjärvi, and R. Sobotka
NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

Scientific Reports

P. Amengual-Rigo, and V. Guallar
SARS-CoV-2 interaction with Siglec-1 mediates trans-infection by dendritic cells

Cellular & Molecular Immunology

D. Perez-Zsolt, J. Muñoz-Basagoiti, J. Rodon, M. Elosua-Bayes, D. Raïch-Regué, C. Risco, M. Sachse, M. Pino, S. Gumber, M. Paiardini, J. Chojnacki, I. Erkizia, X. Muñiz-Trabudua, E. Ballana, E. Riveira-Muñoz, M. Noguera-Julian, R. Paredes, B. Trinité, F. Tarrés-Freixas, I. Blanco, V. Guallar, J. Carrillo, J. Blanco, A. Telenti, H. Heyn, J. Segalés, B. Clotet, J. Martinez-Picado, J. Vergara-Alert, and N. Izquierdo-Useros

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