Kam Y. J. Zhang

Publication Activity (10 Years)

Years Active: 2010-2022
Publications (10 Years): 16

Top Topics

Shape Similarity

Intrinsically Disordered

Virtual Screening

Translation Invariant

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

Briefings Bioinform.

J. Cheminformatics

Publications

Rahul Kaushik, Kam Y. J. Zhang
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures. Bioinform. 38 (2) (2022)
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
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Briefings Bioinform. 22 (2) (2021)
Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Sonia Longhi, Kam Y. J. Zhang, Sandeep Bhatia
Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Briefings Bioinform. 22 (5) (2021)
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
An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. Briefings Bioinform. 22 (6) (2021)
Francois Berenger, Ashutosh Kumar, Kam Y. J. Zhang, Yoshihiro Yamanishi
Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking. J. Chem. Inf. Model. 61 (5) (2021)
David Simoncini, Kam Y. J. Zhang, Thomas Schiex, Sophie Barbe
A structural homology approach for computational protein design with flexible backbone. Bioinform. 35 (14) (2019)
Ashutosh Kumar, Kam Y. J. Zhang
Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. J. Comput. Aided Mol. Des. 33 (1) (2019)
Francois Berenger, Kam Y. J. Zhang, Yoshihiro Yamanishi
Chemoinformatics and structural bioinformatics in OCaml. J. Cheminformatics 11 (1) (2019)
Ashutosh Kumar, Kam Y. J. Zhang
Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model. J. Comput. Aided Mol. Des. 33 (12) (2019)
Ashutosh Kumar, Kam Y. J. Zhang
A cross docking pipeline for improving pose prediction and virtual screening performance. J. Comput. Aided Mol. Des. 32 (1) (2018)
Francois Berenger, David Simoncini, Arnout R. D. Voet, Rojan Shrestha, Kam Y. J. Zhang
Fragger: a protein fragment picker for structural queries. F1000Research 6 (2017)
Masaki Matsuoka, Ashutosh Kumar, Muhammad Muddassar, Akihisa Matsuyama, Minoru Yoshida, Kam Y. J. Zhang
. J. Chem. Inf. Model. 57 (2) (2017)
Ashutosh Kumar, Kam Y. J. Zhang
A pose prediction approach based on ligand 3D shape similarity. J. Comput. Aided Mol. Des. 30 (6) (2016)
Ashutosh Kumar, Kam Y. J. Zhang
Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. J. Chem. Inf. Model. 56 (6) (2016)
Xi Jiang, Ashutosh Kumar, Tian Liu, Kam Y. J. Zhang, Qing Yang
A Novel Scaffold for Developing Specific or Broad-Spectrum Chitinase Inhibitors. J. Chem. Inf. Model. 56 (12) (2016)
Ashutosh Kumar, Kam Y. J. Zhang
Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. 30 (9) (2016)
Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang
Identification of SUMO activating enzyme 1 inhibitors utilizing virtual screening approach. J. Cheminformatics 6 (S-1) (2014)
Arnout R. D. Voet, Ashutosh Kumar, Francois Berenger, Kam Y. J. Zhang
Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. J. Comput. Aided Mol. Des. 28 (4) (2014)
Ashutosh Kumar, Akihiro Ito, Misao Takemoto, Minoru Yoshida, Kam Y. J. Zhang
Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening. J. Chem. Inf. Model. 54 (3) (2014)
Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang
Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9. J. Chem. Inf. Model. 54 (10) (2014)
Francois Berenger, Arnout R. D. Voet, Xiao Yin Lee, Kam Y. J. Zhang
A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. J. Cheminformatics 6 (1) (2014)
Ashutosh Kumar, Kam Y. J. Zhang
Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise. J. Chem. Inf. Model. 53 (8) (2013)
Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang
Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening. J. Chem. Inf. Model. 53 (4) (2013)
Ashutosh Kumar, Kam Y. J. Zhang
Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge. J. Comput. Aided Mol. Des. 26 (5) (2012)
Francois Berenger, Rojan Shrestha, Yong Zhou, David Simoncini, Kam Y. J. Zhang
Durandal: Fast exact clustering of protein decoys. J. Comput. Chem. 33 (4) (2012)
Francois Berenger, Yong Zhou, Rojan Shrestha, Kam Y. J. Zhang
Entropy-accelerated exact clustering of protein decoys. Bioinform. 27 (7) (2011)
Francois Berenger, Camille Coti, Kam Y. J. Zhang
PAR: a PARallel and distributed job crusher. Bioinform. 26 (22) (2010)