Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2012)

Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening. - Ashutosh Kumar 001; Akihiro Ito; Mikako Hirohama; Minoru Yoshida; Kam Y. J. Zhang (J. Chem. Inf. Model., 2013)

Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Chem. Inf. Model., 2013)

Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. - Arnout R. D. Voet; Ashutosh Kumar 001; Francois Berenger; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2014)

Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach. - Ashutosh Kumar 001; Akihiro Ito; Mikako Hirohama; Minoru Yoshida; Kam Y. J. Zhang (J. Cheminformatics, 2014)

Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9. - Ashutosh Kumar 001; Akihiro Ito; Mikako Hirohama; Minoru Yoshida; Kam Y. J. Zhang (J. Chem. Inf. Model., 2014)

Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening. - Ashutosh Kumar 001; Akihiro Ito; Misao Takemoto; Minoru Yoshida; Kam Y. J. Zhang (J. Chem. Inf. Model., 2014)

A pose prediction approach based on ligand 3D shape similarity. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2016)

Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2016)

Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Chem. Inf. Model., 2016)

A Novel Scaffold for Developing Specific or Broad-Spectrum Chitinase Inhibitors. - Xi Jiang; Ashutosh Kumar 001; Tian Liu; Kam Y. J. Zhang; Qing Yang (J. Chem. Inf. Model., 2016)

Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum. - Masaki Matsuoka; Ashutosh Kumar 001; Muhammad Muddassar; Akihisa Matsuyama; Minoru Yoshida; Kam Y. J. Zhang (J. Chem. Inf. Model., 2017)

A cross docking pipeline for improving pose prediction and virtual screening performance. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2018)

Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2019)

Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model. - Ashutosh Kumar 001; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2019)

An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. - Aditya K. Padhi; Ashutosh Kumar 001; Ken-ichi Haruna; Haruna Sato; Hiroko Tamura; Satoru Nagatoishi; Kouhei Tsumoto; Atushi Yamaguchi; Fumie Iraha; Mihoko Takahashi; Kensaku Sakamoto; Kam Y. J. Zhang (Briefings Bioinform., 2021)

Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking. - Francois Berenger; Ashutosh Kumar 001; Kam Y. J. Zhang; Yoshihiro Yamanishi (J. Chem. Inf. Model., 2021)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)