PAR: a PARallel and distributed job crusher. - Francois Berenger; Camille Coti; Kam Y. J. Zhang (Bioinform., 2010)

Entropy-accelerated exact clustering of protein decoys. - Francois Berenger; Yong Zhou; Rojan Shrestha; Kam Y. J. Zhang (Bioinform., 2011)

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

Durandal: Fast exact clustering of protein decoys. - Francois Berenger; Rojan Shrestha; Yong Zhou; David Simoncini; Kam Y. J. Zhang (J. Comput. Chem., 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)

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. - Francois Berenger; Arnout R. D. Voet; Xiao Yin Lee; Kam Y. J. Zhang (J. Cheminformatics, 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)

Fragger: a protein fragment picker for structural queries. - Francois Berenger; David Simoncini; Arnout R. D. Voet; Rojan Shrestha; Kam Y. J. Zhang (F1000Research, 2017)

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)

A structural homology approach for computational protein design with flexible backbone. - David Simoncini; Kam Y. J. Zhang; Thomas Schiex; Sophie Barbe (Bioinform., 2019)

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)

Chemoinformatics and structural bioinformatics in OCaml. - Francois Berenger; Kam Y. J. Zhang; Yoshihiro Yamanishi (J. Cheminformatics, 2019)

Population-Based Sampling and Fragment-Based De Novo Protein Structure Prediction. - David Simoncini; Kam Y. J. Zhang (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. - Naveen Kumar; Rahul Kaushik; Chandana Tennakoon; Vladimir N. Uversky; Sonia Longhi; Kam Y. J. Zhang; Sandeep Bhatia (Briefings Bioinform., 2021)

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. - Yashpal Singh Malik; Mohd Ikram Ansari; Jobin Jose Kattoor; Rahul Kaushik; Shubhankar Sircar; Anbazhagan Subbaiyan; Ruchi Tiwari; Kuldeep Dhama; Souvik Ghosh; Shailly Tomar; Kam Y. J. Zhang (Briefings Bioinform., 2021)

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)

ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. - Rahul Kaushik; Kam Y. J. Zhang (Bioinform., 2022)

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)