Kam Y. J. Zhang

29 papers Journal 28

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. J. Chem. Inf. Model. 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, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled M. Edwards, Merveille K. I. Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S. Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J. Irwin, Olexandr Isayev, Aleksandra Ivanova, Célien Jacquemard, Austin J. Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta F. Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J. Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel G. Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina E. M. Schindler, François Sindt, Vojtech Spiwok, Casper Steinmann, Rick L. Stevens, Valerij Talagayev, Damon Tingey, Oanh Vu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, Matthieu Schapira
2022	J	`jnl`	ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. Bioinform. Rahul Kaushik, Kam Y. J. Zhang
2021	J	`jnl`	An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. Briefings Bioinform. Aditya K. Padhi, Ashutosh Kumar, Ken-ichi Haruna, Haruna Sato, Hiroko Tamura, Satoru Nagatoishi, Kouhei Tsumoto, Atushi Yamaguchi, Fumie Iraha, Mihoko Takahashi, Kensaku Sakamoto, Kam Y. J. Zhang
2021	J	`jnl`	Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Briefings Bioinform. 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
2021	J	`jnl`	Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Briefings Bioinform. Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Sonia Longhi, Kam Y. J. Zhang, Sandeep Bhatia
2021	J	`jnl`	Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking. J. Chem. Inf. Model. Francois Berenger, Ashutosh Kumar, Kam Y. J. Zhang, Yoshihiro Yamanishi
2019	J	`jnl`	A structural homology approach for computational protein design with flexible backbone. Bioinform. David Simoncini, Kam Y. J. Zhang, Thomas Schiex, Sophie Barbe
2019	J	`jnl`	Chemoinformatics and structural bioinformatics in OCaml. J. Cheminformatics Francois Berenger, Kam Y. J. Zhang, Yoshihiro Yamanishi
2019	J	`jnl`	Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model. J. Comput. Aided Mol. Des. Ashutosh Kumar, Kam Y. J. Zhang
2019	—	`ch.`	Population-Based Sampling and Fragment-Based De Novo Protein Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (1) David Simoncini, Kam Y. J. Zhang
2019	J	`jnl`	Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. J. Comput. Aided Mol. Des. Ashutosh Kumar, Kam Y. J. Zhang
2018	J	`jnl`	A cross docking pipeline for improving pose prediction and virtual screening performance. J. Comput. Aided Mol. Des. Ashutosh Kumar, Kam Y. J. Zhang
2017	J	`jnl`	Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from J. Chem. Inf. Model. Masaki Matsuoka, Ashutosh Kumar, Muhammad Muddassar, Akihisa Matsuyama, Minoru Yoshida, Kam Y. J. Zhang
2017	J	`jnl`	Fragger: a protein fragment picker for structural queries. F1000Research Francois Berenger, David Simoncini, Arnout R. D. Voet, Rojan Shrestha, Kam Y. J. Zhang
2016	J	`jnl`	A Novel Scaffold for Developing Specific or Broad-Spectrum Chitinase Inhibitors. J. Chem. Inf. Model. Xi Jiang, Ashutosh Kumar, Tian Liu, Kam Y. J. Zhang, Qing Yang
2016	J	`jnl`	A pose prediction approach based on ligand 3D shape similarity. J. Comput. Aided Mol. Des. Ashutosh Kumar, Kam Y. J. Zhang
2016	J	`jnl`	Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. J. Chem. Inf. Model. Ashutosh Kumar, Kam Y. J. Zhang
2016	J	`jnl`	Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. Ashutosh Kumar, Kam Y. J. Zhang
2014	J	`jnl`	A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. J. Cheminformatics Francois Berenger, Arnout R. D. Voet, Xiao Yin Lee, Kam Y. J. Zhang
2014	J	`jnl`	Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. J. Comput. Aided Mol. Des. Arnout R. D. Voet, Ashutosh Kumar, Francois Berenger, Kam Y. J. Zhang
2014	J	`jnl`	Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening. J. Chem. Inf. Model. Ashutosh Kumar, Akihiro Ito, Misao Takemoto, Minoru Yoshida, Kam Y. J. Zhang
2014	J	`jnl`	Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach. J. Cheminformatics Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang
2014	J	`jnl`	Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9. J. Chem. Inf. Model. Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang
2013	J	`jnl`	Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening. J. Chem. Inf. Model. Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang
2013	J	`jnl`	Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise. J. Chem. Inf. Model. Ashutosh Kumar, Kam Y. J. Zhang
2012	J	`jnl`	Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge. J. Comput. Aided Mol. Des. Ashutosh Kumar, Kam Y. J. Zhang
2012	J	`jnl`	Durandal: Fast exact clustering of protein decoys. J. Comput. Chem. Francois Berenger, Rojan Shrestha, Yong Zhou, David Simoncini, Kam Y. J. Zhang
2011	J	`jnl`	Entropy-accelerated exact clustering of protein decoys. Bioinform. Francois Berenger, Yong Zhou, Rojan Shrestha, Kam Y. J. Zhang
2010	J	`jnl`	PAR: a PARallel and distributed job crusher. Bioinform. Francois Berenger, Camille Coti, Kam Y. J. Zhang