On the suitability of semiempirical calculations as sources of force field parameters. - Carlos Alemán; Modesto Orozco (J. Comput. Aided Mol. Des., 1992)

A new scaling procedure to correct semiempirical MEP and MEP-derived properties. - Carlos Alemán; F. Javier Luque; Modesto Orozco (J. Comput. Aided Mol. Des., 1993)

SCF-MO study of the polyglycine II structure. - Carlos Alemán; Juan Jesús Pérez (J. Comput. Aided Mol. Des., 1993)

Suitability of the PM3-derived molecular electrostatic potentials. - Carlos Alemán; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 1993)

A quantum-mechanical study of the chain-length dependent stability of the extended and 310-helix conformations in dehydroalanine oligopeptides. - Jordi Casanovas; Carlos Alemán (J. Comput. Aided Mol. Des., 1994)

Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4. - F. Javier Luque; Margarida Bachs; Carlos Alemán; Modesto Orozco (J. Comput. Chem., 1996)

PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. - Carlos Alemán; Jordi Casanovas; Sérgio Emanuel Galembeck (J. Comput. Aided Mol. Des., 1998)

Force-field parametrization and molecular dynamics simulations of p-menthan-3, 9-diols: a family of amphiphilic compounds derived from terpenoids. - Adriana M. Namba; Salvador León; Gil Valdo José da Silva; Carlos Alemán (J. Comput. Aided Mol. Des., 2001)

MCDP: an advanced tool to simulate comb-like polymers. - Salvador León; Carlos Alemán; Francesc Escalé; Manuel Laso (J. Comput. Chem., 2001)

Influence of the presence of small gas molecules in the structure of comblike polyacrylates: A Monte Carlo study. - Salvador León; David Zanuy; Carlos Alemán (J. Comput. Chem., 2002)

EVEBAT: A fast strategy for the examination of the empty space in polymer matrices. - David Curcó; David Zanuy; Carlos Alemán (J. Comput. Chem., 2003)

Thermally induced phase transition in helical comblike poly(-peptide)s: An atomistic simulation. - David Zanuy; Carlos Alemán; Manuel Laso; Sebastián Muñoz-Guerra (J. Comput. Chem., 2003)

Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima. - David Curcó; Carlos Alemán (J. Comput. Chem., 2004)

A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima. - David Curcó; Jordi Casanovas; Marc Roca; Carlos Alemán (Comput. Phys. Commun., 2005)

Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters. - David Curcó; Francisco Rodríguez-Ropero; Carlos Alemán (J. Comput. Aided Mol. Des., 2006)

Computational tool to model the packing of polycyclic chains: Structural analysis of amorphous polythiophene. - David Curcó; Carlos Alemán (J. Comput. Chem., 2007)

Coarse-graining: A procedure to generate equilibrated and relaxed models of amorphous polymers. - David Curcó; Carlos Alemán (J. Comput. Chem., 2007)

Ab initio calculations on pi-stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters. - Francisco Rodríguez-Ropero; Jordi Casanovas; Carlos Alemán (J. Comput. Chem., 2008)

Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle. - Francisco Rodríguez-Ropero; David Zanuy; Carlos Alemán (J. Comput. Chem., 2008)

Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design. - Francisco Rodríguez-Ropero; David Zanuy; Jordi Casanovas; Ruth Nussinov; Carlos Alemán (J. Chem. Inf. Model., 2008)

Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale. - David Zanuy; Gema Ballano; Ana I. Jiménez; Jordi Casanovas; Nurit Haspel; Carlos Cativiela; David Curcó; Ruth Nussinov; Carlos Alemán (J. Chem. Inf. Model., 2009)

Parameterization of the torsional potential for calix[4]arene-substituted poly(thiophene)s. - Julien Preat; Francisco Rodríguez-Ropero; Juan Torras; Oscar Bertran; David Zanuy; Carlos Alemán (J. Comput. Chem., 2010)

Conformational Profile of a Proline-Arginine Hybrid. - Guillem Revilla-López; Ana I. Jiménez; Carlos Cativiela; Ruth Nussinov; Carlos Alemán; David Zanuy (J. Chem. Inf. Model., 2010)

A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: Application to peptides. - David Curcó; David Zanuy; Ruth Nussinov; Carlos Alemán (J. Comput. Chem., 2011)

Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing. - David Zanuy; Francisco J. Sayago; Guillem Revilla-López; Gema Ballano; Lilach Agemy; Venkata Ramana Kotamraju; Ana I. Jiménez; Carlos Cativiela; Ruth Nussinov; April M. Sawvel; Galen Stucky; Erkki Ruoslahti; et al. (J. Comput. Aided Mol. Des., 2013)

IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study. - Didac Martí; Carlos Alemán; Jon Ainsley; Oscar Ahumada; Juan Torras (J. Chem. Inf. Model., 2022)

Intelligent cross-linking in polymer simulations: SuSi's approach to complex 3D networks. - David Naranjo; Didac Martí; Carlos Alemán; Jose Garcia-Torres; Juan Torras (Comput. Phys. Commun., 2025)