Kam Y J Zhang

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 47

Top Topics

Structure Activity Relationship

Crystal Structure

Molecular Docking

Top Venues

Nature communications

Communications biology

This page only lists publications with an associated author ORCID identifier.

Publications

Naveen Kumar, Rahul Kaushik, Kam Y J Zhang, Vladimir N Uversky, Upasana Sahu, Richa Sood, Sandeep Bhatia
A novel consensus-based computational pipeline for screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant. Proteins (2023)
Kosaku Okuda, Kengo Nakahara, Akihiro Ito, Yuta Iijima, Ryosuke Nomura, Ashutosh Kumar, Kana Fujikawa, Kazuya Adachi, Yuki Shimada, Satoshi Fujio, Reina Yamamoto, Nobumasa Takasugi, Kunishige Onuma, Mitsuhiko Osaki, Futoshi Okada, Taichi Ukegawa, Yasuo Takeuchi, Norihisa Yasui, Atsuko Yamashita, Hiroyuki Marusawa, Yosuke Matsushita, Toyomasa Katagiri, Takahiro Shibata, Koji Uchida, Sheng-Yong Niu, Nhi B Lang, Tomohiro Nakamura, Kam Y J Zhang, Stuart A Lipton, Takashi Uehara
Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature communications 14 (1) (2023)
Chunlai Tam, Mutsuko Kukimoto-Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, Mio Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto, Mikako Shirouzu, Kam Y J Zhang
Targeting Ras-binding domain of ELMO1 by computational nanobody design. Communications biology 6 (1) (2023)
Ashutosh Kumar, Masaki Matsuoka, Akihisa Matsuyama, Minoru Yoshida, Kam Y J Zhang
Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase. Journal of agricultural and food chemistry (2023)
Kosaku Okuda, Kengo Nakahara, Akihiro Ito, Yuta Iijima, Ryosuke Nomura, Ashutosh Kumar, Kana Fujikawa, Kazuya Adachi, Yuki Shimada, Satoshi Fujio, Reina Yamamoto, Nobumasa Takasugi, Kunishige Onuma, Mitsuhiko Osaki, Futoshi Okada, Taichi Ukegawa, Yasuo Takeuchi, Norihisa Yasui, Atsuko Yamashita, Hiroyuki Marusawa, Yosuke Matsushita, Toyomasa Katagiri, Takahiro Shibata, Koji Uchida, Sheng-Yong Niu, Nhi B Lang, Tomohiro Nakamura, Kam Y J Zhang, Stuart A Lipton, Takashi Uehara
Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature communications 14 (1) (2023)
Chunlai Tam, Mutsuko Kukimoto-Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, Mio Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto, Mikako Shirouzu, Kam Y J Zhang
Targeting Ras-binding domain of ELMO1 by computational nanobody design. Communications biology 6 (1) (2023)
Kosaku Okuda, Kengo Nakahara, Akihiro Ito, Yuta Iijima, Ryosuke Nomura, Ashutosh Kumar, Kana Fujikawa, Kazuya Adachi, Yuki Shimada, Satoshi Fujio, Reina Yamamoto, Nobumasa Takasugi, Kunishige Onuma, Mitsuhiko Osaki, Futoshi Okada, Taichi Ukegawa, Yasuo Takeuchi, Norihisa Yasui, Atsuko Yamashita, Hiroyuki Marusawa, Yosuke Matsushita, Toyomasa Katagiri, Takahiro Shibata, Koji Uchida, Sheng-Yong Niu, Nhi B Lang, Tomohiro Nakamura, Kam Y J Zhang, Stuart A Lipton, Takashi Uehara
Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature communications 14 (1) (2023)
Chunlai Tam, Mutsuko Kukimoto-Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, Mio Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto, Mikako Shirouzu, Kam Y J Zhang
Targeting Ras-binding domain of ELMO1 by computational nanobody design. Communications biology 6 (1) (2023)
Kosaku Okuda, Kengo Nakahara, Akihiro Ito, Yuta Iijima, Ryosuke Nomura, Ashutosh Kumar, Kana Fujikawa, Kazuya Adachi, Yuki Shimada, Satoshi Fujio, Reina Yamamoto, Nobumasa Takasugi, Kunishige Onuma, Mitsuhiko Osaki, Futoshi Okada, Taichi Ukegawa, Yasuo Takeuchi, Norihisa Yasui, Atsuko Yamashita, Hiroyuki Marusawa, Yosuke Matsushita, Toyomasa Katagiri, Takahiro Shibata, Koji Uchida, Sheng-Yong Niu, Nhi B Lang, Tomohiro Nakamura, Kam Y J Zhang, Stuart A Lipton, Takashi Uehara
Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature communications 14 (1) (2023)
Chunlai Tam, Mutsuko Kukimoto-Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, Mio Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto, Mikako Shirouzu, Kam Y J Zhang
Targeting Ras-binding domain of ELMO1 by computational nanobody design. Communications biology 6 (1) (2023)
Chunlai Tam, Mutsuko Kukimoto-Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, Mio Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto, Mikako Shirouzu, Kam Y J Zhang
Targeting Ras-binding domain of ELMO1 by computational nanobody design. Communications biology 6 (1) (2023)
Kosaku Okuda, Kengo Nakahara, Akihiro Ito, Yuta Iijima, Ryosuke Nomura, Ashutosh Kumar, Kana Fujikawa, Kazuya Adachi, Yuki Shimada, Satoshi Fujio, Reina Yamamoto, Nobumasa Takasugi, Kunishige Onuma, Mitsuhiko Osaki, Futoshi Okada, Taichi Ukegawa, Yasuo Takeuchi, Norihisa Yasui, Atsuko Yamashita, Hiroyuki Marusawa, Yosuke Matsushita, Toyomasa Katagiri, Takahiro Shibata, Koji Uchida, Sheng-Yong Niu, Nhi B Lang, Tomohiro Nakamura, Kam Y J Zhang, Stuart A Lipton, Takashi Uehara
Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature communications 14 (1) (2023)
Naveen Kumar, Rahul Kaushik, Kam Y J Zhang, Vladimir N Uversky, Upasana Sahu, Richa Sood, Sandeep Bhatia
A novel consensus-based computational pipeline for screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant. Proteins (2023)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Almasul Alfi, Aleksandr Popov, Ashutosh Kumar, Kam Y J Zhang, Svetlana Dubiley, Konstantin Severinov, Shunsuke Tagami
Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2. ACS synthetic biology 11 (6) (2022)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N Uversky, Kam Y J Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal
Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages. Viruses 14 (12) (2022)
Francois Berenger, Ashutosh Kumar, Kam Y J Zhang, Yoshihiro Yamanishi
Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking. Journal of chemical information and modeling 61 (5) (2021)
Shabeesh Balan, Yoshimi Iwayama, Tetsuo Ohnishi, Mikiko Fukuda, Atsuko Shirai, Ayumi Yamada, Sara Weirich, Maren Kirstin Schuhmacher, Kalarickal Vijayan Dileep, Toshihiro Endo, Yasuko Hisano, Kaoru Kotoshiba, Tomoko Toyota, Takeshi Otowa, Hitoshi Kuwabara, Mamoru Tochigi, Akiko Watanabe, Hisako Ohba, Motoko Maekawa, Manabu Toyoshima, Tsukasa Sasaki, Kazuhiko Nakamura, Masatsugu Tsujii, Hideo Matsuzaki, Kam Y J Zhang, Albert Jeltsch, Yoichi Shinkai, Takeo Yoshikawa
A loss-of-function variant in SUV39H2 identified in autism-spectrum disorder causes altered H3K9 trimethylation and dysregulation of protocadherin β-cluster genes in the developing brain. Molecular psychiatry (2021)
Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N Uversky, Sonia Longhi, Kam Y J Zhang, Sandeep Bhatia
Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins. Journal of proteome research 20 (5) (2021)
Jeroen P M Vrancken, Hiroki Noguchi, Kam Y J Zhang, Jeremy R H Tame, Arnout R D Voet
The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins (2021)
Sota Yagi, Aditya K Padhi, Jelena Vucinic, Sophie Barbe, Thomas Schiex, Reiko Nakagawa, David Simoncini, Kam Y J Zhang, Shunsuke Tagami
Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. Journal of the American Chemical Society 143 (39) (2021)
Matej Janežič, Kalarickal V Dileep, Kam Y J Zhang
A multidimensional computational exploration of congenital myasthenic syndrome causing mutations in human choline acetyltransferase. Journal of cellular biochemistry 122 (8) (2021)
Nitin Chitranshi, Ashutosh Kumar, Samran Sheriff, Veer Gupta, Angela Godinez, Danit Saks, Soumalya Sarkar, Ting Shen, Mehdi Mirzaei, Devaraj Basavarajappa, Morteza Abyadeh, Dinesh Kumar Chellapan, Kamal Dua, Kam Y J Zhang, Stuart L Graham, Vivek Gupta
Identification of Novel Cathepsin B Inhibitors with Implications in Alzheimer's Disease: Computational Refining and Biochemical Evaluation. Cells 10 (8) (2021)
Qi Chen, Wei Chen, Ashutosh Kumar, Xi Jiang, Matej Janezic, Kam Y J Zhang, Qing Yang
Crystal Structure and Structure-Based Discovery of Inhibitors of the Nematode Chitinase CeCht1. Journal of agricultural and food chemistry 69 (11) (2021)
Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N Uversky, Anamika Mishra, Richa Sood, Pratiksha Srivastava, Meghna Tripathi, Kam Y J Zhang, Sandeep Bhatia
Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species. Viruses 13 (9) (2021)
Chunlai Tam, Ashutosh Kumar, Kam Y J Zhang
NbX: Machine Learning-Guided Re-Ranking of Nanobody-Antigen Binding Poses. Pharmaceuticals (Basel, Switzerland) 14 (10) (2021)
Motoi Yamashita, Hye Sun Kuehn, Kazuki Okuyama, Satoshi Okada, Yuzaburo Inoue, Noriko Mitsuiki, Kohsuke Imai, Masatoshi Takagi, Hirokazu Kanegane, Masahiro Takeuchi, Naoki Shimojo, Miyuki Tsumura, Aditya K Padhi, Kam Y J Zhang, Bertrand Boisson, Jean Laurent Casanova, Osamu Ohara, Sergio D Rosenzweig, Ichiro Taniuchi, Tomohiro Morio
A variant in human AIOLOS impairs adaptive immunity by interfering with IKAROS. Nature immunology 22 (7) (2021)
Erma Fatiha Muhammad, Ashutosh Kumar, Habibah A Wahab, Kam Y J Zhang
Identification of 1,2,4-Triazolylthioethanone Scaffold for the Design of New Acetylcholinesterase Inhibitors. Molecular informatics 40 (8) (2021)
Chunlai Tam, Kam Y J Zhang
FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins. Proteins (2021)
Mutsuko Kukimoto-Niino, Kazushige Katsura, Rahul Kaushik, Haruhiko Ehara, Takeshi Yokoyama, Tomomi Uchikubo-Kamo, Reiko Nakagawa, Chiemi Mishima-Tsumagari, Mayumi Yonemochi, Mariko Ikeda, Kazuharu Hanada, Kam Y J Zhang, Mikako Shirouzu
Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex. Science advances 7 (30) (2021)
Xi Jiang, Ashutosh Kumar, Yasutaka Motomura, Tian Liu, Yong Zhou, Kazuyo Moro, Kam Y J Zhang, Qing Yang
A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors. Journal of medicinal chemistry 63 (3) (2020)
Yoshitomo Shiroma, Go Fujita, Takuya Yamamoto, Ryou-U Takahashi, Ashutosh Kumar, Kam Y J Zhang, Akihiro Ito, Hiroyuki Osada, Minoru Yoshida, Hidetoshi Tahara
Identification of a Selective RelA Inhibitor Based on DSE-FRET Screening Methods. International journal of molecular sciences 21 (23) (2020)
Rahul Kaushik, Kam Y J Zhang
A protein sequence fitness function for identifying natural and nonnatural proteins. Proteins 88 (10) (2020)
Hareesh B Nair, Bindu Santhamma, Kalarickal V Dileep, Peter Binkley, Kirk Acosta, Kam Y J Zhang, Robert Schenken, Klaus Nickisch
EC313-a tissue selective SPRM reduces the growth and proliferation of uterine fibroids in a human uterine fibroid tissue xenograft model. Scientific reports 9 (1) (2019)
Ashutosh Kumar, Kam Y J Zhang
Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model. Journal of computer-aided molecular design 33 (12) (2019)
Hiroki Noguchi, Christine Addy, David Simoncini, Staf Wouters, Bram Mylemans, Luc Van Meervelt, Thomas Schiex, Kam Y J Zhang, Jeremy R H Tame, Arnout R D Voet
Computational design of symmetrical eight-bladed β-propeller proteins. IUCrJ 6 (Pt 1) (2019)
Ashutosh Kumar, Kam Y J Zhang
Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3. Journal of computer-aided molecular design 33 (1) (2018)
Francois Berenger, David Simoncini, Arnout Voet, Rojan Shrestha, Kam Y J Zhang
Fragger: a protein fragment picker for structural queries. F1000Research (2017)
Ashutosh Kumar, Kam Y J Zhang
A cross docking pipeline for improving pose prediction and virtual screening performance. Journal of computer-aided molecular design 32 (1) (2017)
Daiki Terada, Arnout R D Voet, Hiroki Noguchi, Kenichi Kamata, Mio Ohki, Christine Addy, Yuki Fujii, Daiki Yamamoto, Yasuhiro Ozeki, Jeremy R H Tame, Kam Y J Zhang
Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity. Scientific reports 7 (1) (2017)
Francois Berenger, David Simoncini, Arnout 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
Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum. Journal of chemical information and modeling 57 (2) (2017)