MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening. - Shuangye Yin; Lada Biedermannová; Jirí Vondrásek; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2008)

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands. - Feng Ding 002; Shuangye Yin; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2010)

Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets. - Jui-Hua Hsieh; Shuangye Yin; Shubin Liu; Alexander Sedykh; Nikolay V. Dokholyan; Alexander Tropsha (J. Chem. Inf. Model., 2011)

Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening. - Jui-Hua Hsieh; Shuangye Yin; Xiang S. Wang; Shubin Liu; Nikolay V. Dokholyan; Alexander Tropsha (J. Chem. Inf. Model., 2012)