Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach. - Art E. Cho; Victor Guallar; Bruce J. Berne; Richard A. Friesner (J. Comput. Chem., 2005)

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. - Kenneth W. Borrelli; Benjamin P. Cossins; Victor Guallar (J. Comput. Chem., 2010)

A New View of the Bacterial Cytosol Environment. - Benjamin P. Cossins; Matthew P. Jacobson; Victor Guallar (PLoS Comput. Biol., 2011)

pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling. - Víctor A. Gil; Victor Guallar (Bioinform., 2013)

PELE web server: atomistic study of biomolecular systems at your fingertips. - Armin Madadkar-Sobhani; Victor Guallar (Nucleic Acids Res., 2013)

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase - Cytochrome c. - Frank H. Wallrapp; Alexander A. Voityuk; Victor Guallar (PLoS Comput. Biol., 2013)

Correlated Inter-Domain Motions in Adenylate Kinase. - Santiago Esteban-Martín; Robert Bryn Fenwick; Jörgen Ådén; Benjamin P. Cossins; Carlos W. Bertoncini; Victor Guallar; Magnus Wolf-Watz; Xavier Salvatella (PLoS Comput. Biol., 2014)

Instant Visualization of Secondary Structures of Molecular Models. - Pedro Hermosilla; Victor Guallar; Àlvar Vinacua; Pere-Pau Vázquez (VCBM, 2015)

High quality illustrative effects for molecular rendering. - Pedro Hermosilla; Victor Guallar; Àlvar Vinacua; Pere-Pau Vázquez (Comput. Graph., 2016)

Ecoupling server: A tool to compute and analyze electronic couplings. - Israel Cabeza de Vaca; Sandra Acebes; Victor Guallar (J. Comput. Chem., 2016)

Computational Prediction of HIV-1 Resistance to Protease Inhibitors. - Ali Hosseini; Andreu Alibés; Marc Noguera-Julian; Víctor A. Gil; Roger Paredes; Robert Soliva; Modesto Orozco; Victor Guallar (J. Chem. Inf. Model., 2016)

Real-Time Molecular Visualization Supporting Diffuse Interreflections and Ambient Occlusion. - Robin Skånberg; Pere-Pau Vázquez; Victor Guallar; Timo Ropinski (IEEE Trans. Vis. Comput. Graph., 2016)

The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths. - Gudrun Gygli; Maria Fátima Lucas; Victor Guallar; Willem J. H. van Berkel (PLoS Comput. Biol., 2017)

Physics-Based Visual Characterization of Molecular Interaction Forces. - Pedro Hermosilla; Jorge Estrada; Victor Guallar; Timo Ropinski; Àlvar Vinacua; Pere-Pau Vázquez (IEEE Trans. Vis. Comput. Graph., 2017)

Interactive GPU-based generation of solvent-excluded surfaces. - Pedro Hermosilla; Michael Krone; Victor Guallar; Pere-Pau Vázquez; Àlvar Vinacua; Timo Ropinski (Vis. Comput., 2017)

Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs. - Martin Kotev; Pilar Manuel-Manresa; Elsa Hernando; Vanessa Soto-Cerrato; Modesto Orozco; Roberto Quesada; Ricardo Pérez-Tomás; Victor Guallar (J. Chem. Inf. Model., 2017)

Visual Analysis of protein-ligand interactions. - Pere-Pau Vázquez; Pedro Hermosilla; Victor Guallar; Jorge Estrada; Àlvar Vinacua (Comput. Graph. Forum, 2018)

Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case. - Martin Kotev; Rosalia Pascual; Carmen Almansa; Victor Guallar; Robert Soliva (J. Chem. Inf. Model., 2018)

Combining Monte Carlo and Molecular Dynamics Simulations for Enhanced Binding Free Energy Estimation through Markov State Models. - Joan F. Gilabert; Oriol Gracia Carmona; Anders Hogner; Victor Guallar (J. Chem. Inf. Model., 2020)

FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design. - Carles Perez; Daniel Soler; Robert Soliva; Victor Guallar (J. Chem. Inf. Model., 2020)

UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. - Pep Amengual-Rigo; Juan Fernández-Recio; Victor Guallar (Bioinform., 2021)

Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures. - Thijs Beuming; Helena Martín; Anna M. Díaz-Rovira; Lucía Díaz; Victor Guallar; Soumya S. Ray (J. Chem. Inf. Model., 2022)

Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks. - Isaac Filella-Merce; Alexis Molina; Marek Orzechowski; Lucía Díaz; Yang Ming Zhu; Julia Vilalta Mor; Laura Malo; Ajay S. Yekkirala; Soumya S. Ray; Victor Guallar (CoRR, 2023)

Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. - Anna M. Díaz-Rovira; Helena Martín; Thijs Beuming; Lucía Díaz; Victor Guallar; Soumya S. Ray (J. Chem. Inf. Model., 2023)

Scoreformer: A Surrogate Model For Large-Scale Prediction of Docking Scores. - Álvaro Ciudad; Adrián Morales-Pastor; Laura Malo; Isaac Filella-Merce; Victor Guallar; Alexis Molina (CoRR, 2024)

ICML Topological Deep Learning Challenge 2024: Beyond the Graph Domain. - Guillermo Bernárdez; Lev Telyatnikov; Marco Montagna; Federica Baccini; Mathilde Papillon; Miquel Ferriol Galmés; Mustafa Hajij; Theodore Papamarkou; Maria Sofia Bucarelli; Olga Zaghen; Johan Mathe; Audun Myers; et al. (CoRR, 2024)

Active Learning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation. - Julia Vilalta Mor; Alexis Molina; Laura Ortega Varga; Isaac Filella-Merce; Victor Guallar (CoRR, 2025)