Towards an understanding of the molecular basis of hydrophobicity. - Ricardo L. Mancera (J. Comput. Aided Mol. Des., 1996)

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase. - Ricardo L. Mancera (J. Comput. Aided Mol. Des., 2002)

A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein. - Matthew D. Kelly; Ricardo L. Mancera (J. Comput. Aided Mol. Des., 2003)

The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models. - David G. Lloyd; Alfonso T. García-Sosa; Ian L. Alberts; Nikolay P. Todorov; Ricardo L. Mancera (J. Comput. Aided Mol. Des., 2004)

Molecular modelling prediction of ligand binding site flexibility. - Ami Yi-Ching Yang; Per Källblad; Ricardo L. Mancera (J. Comput. Aided Mol. Des., 2004)

Ligand-protein docking using a quantum stochastic tunneling optimization method. - Ricardo L. Mancera; Per Källblad; Nikolay P. Todorov (J. Comput. Chem., 2004)

Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design. - Matthew D. Kelly; Ricardo L. Mancera (J. Chem. Inf. Model., 2004)

Including Tightly-Bound Water Molecules in de Novo Drug Design. Exemplification through the in Silico Generation of Poly(ADP-ribose)polymerase Ligands. - Alfonso T. García-Sosa; Stuart Firth-Clark; Ricardo L. Mancera (J. Chem. Inf. Model., 2005)

Characterization of Sequence and Structural Features of the Candida krusei Enolase. - Neha Gandhi; Kathy Young; John R. Warmington; Ricardo L. Mancera (Silico Biol., 2008)

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein. - Ami Yi-Ching Yang; Ricardo L. Mancera (J. Comput. Aided Mol. Des., 2008)

Ligand-Protein Docking with Water Molecules. - Benjamin C. Roberts; Ricardo L. Mancera (J. Chem. Inf. Model., 2008)

Ligand-Protein Cross-Docking with Water Molecules. - Ramasamy Thilagavathi; Ricardo L. Mancera (J. Chem. Inf. Model., 2010)

Calculations of the Free Energy of Interaction of the c-Fos-c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects. - Zhili Zuo; Neha Gandhi; Ricardo L. Mancera (J. Chem. Inf. Model., 2010)

Molecular Dynamics Simulations of CXCL-8 and Its Interactions with a Receptor Peptide, Heparin Fragments, and Sulfated Linked Cyclitols. - Neha Gandhi; Ricardo L. Mancera (J. Chem. Inf. Model., 2011)

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine. - Michael Wiebrands; Chris J. Malajczuk; Andrew J. Woods; Andrew L. Rohl; Ricardo L. Mancera (J. Integr. Bioinform., 2018)