Electronic and Atomic Protein Modeling (EAPM)

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2022

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
Pigs are not susceptible to SARS‐CoV‐2 infection but are a model for viral immunogenicity studies

Transboundary and Emerging Diseases

J. Vergara‐Alert, J. Rodon, J. Carrillo, N. Te, N. Izquierdo‐Useros, M. Luisa Rodr de la Concepción, C. Ávila‐Nieto, V. Guallar, A. Valencia, G. Cantero, J. Blanco, B. Clotet, A. Bensaid, and J. Segalés
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
Structural basis for substrate specificity of heteromeric transporters of neutral amino acidsSignificance

Proceedings of the National Academy of Sciences

C. F. Rodriguez, P. Escudero-Bravo, L. Díaz, P. Bartoccioni, C. García-Martín, J. G. Gilabert, J. Boskovic, V. Guallar, E. Errasti-Murugarren, O. Llorca, and M. Palacín
Elucidation of ligand binding and dimerization of

Proteins: Structure, Function, and Bioinformatics

H. Sameer, G. Victor, S. Katalin, and A. Henrik
Structural-Based Modeling in Protein Engineering. A Must Do

The Journal of Physical Chemistry B

S. Roda, A. Robles-Martín, R. Xiang, M. Kazemi, and V. Guallar
Structural-Based Modeling in Protein Engineering. A Must Do

The Journal of Physical Chemistry B

S. Roda, A. Robles-Martín, R. Xiang, M. Kazemi, and V. Guallar
Comprehensive Insights into the Production of Long Chain Aliphatic Aldehydes Using a Copper-Radical Alcohol Oxidase as Biocatalys

ACS Sustainable Chemistry & Engineering

D. Ribeaucourt, B. Bissaro, V. Guallar, M. Yemloul, M. Haon, S. Grisel, V. Alphand, H. Brumer, F. Lambert, J-G. Berrin, and M. Lafond
Computationally Driven Rational Design of Substrate Promiscuity on Serine Ester Hydrolases

ACS Catalysis

S. Roda, L. Fernandez-Lopez, R. Cañadas, G. Santiago, M. Ferrer, and V. Guallar

2020

UEP: an open-source and fast classifier for predicting the impact of mutations in protein–protein complexesAbstractMotivationResultsAvailability and implementationSupplementary information

Bioinformatics

P. Amengual-Rigo, J. Fernández-Recio, and V. Guallar
aquaPELE: A Monte Carlo-Based Algorithm to Sample the Effects of Buried Water Molecules in Proteins

Journal of Chemical Theory and Computation

M. Municoy, S. Roda, D. Soler, A. Soutullo, and V. Guallar
FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design

Journal of Chemical Information and Modeling

C. Perez, D. Soler, R. Soliva, and V. Guallar
Sequential oxidation of 5-hydroxymethylfurfural to furan-2,5-dicarboxylic acid by an evolved aryl-alcohol oxidase

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

J. Viña-González, A. T. Martínez, V. Guallar, and M. Alcalde

2018

CHAPTER 10. Modeling O2-dependent Heme Enzymes: A Quick Guide for Non-experts

Dioxygen-dependent Heme Enzymes

F. Sancho, G. Santiago, P. Amengual-Rigo, and V. Guallar
Kauniolide synthase is a P450 with unusual hydroxylation and cyclization-elimination activity

Nature Communications

Q. Liu, A. Beyraghdar Kashkooli, D. Manzano, I. Pateraki, L. Richard, P. Kolkman, M F. Lucas, V. Guallar, R. C. H. de Vos, M. C. R. Franssen, A. van der Krol, and H. Bouwmeester
Automated Design of Efficient and Functionally Diverse Enzyme Repertoires

Molecular Cell

O. Khersonsky, R. Lipsh, Z. Avizemer, iv, Y. Ashani, M. Goldsmith, H. Leader, O. Dym, S. Rogotner, D. L. Trudeau, J. Prilusky, P. Amengual-Rigo, V. Guallar, D. S. Tawfik, and S. J. Fleishman
Description of a Non-Canonical Mn(II)-Oxidation Site in Peroxidases

ACS Catalysis

E. Fernández-Fueyo, I. Davó-Siguero, D. Almendral, D. Linde, M C. Baratto, R. Pogni, A. Romero, V. Guallar, and A. T. Martínez
Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case

Journal of Chemical Information and Modeling

M. Kotev, R. Pascual, C. Almansa,