Recent Advances of the Fragment Molecular Orbital Method

1. Front Matter

   Pages i-xi

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2. Positioning of FMO

   1. Front Matter

      Pages 1-1

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   2. Fragment Molecular Orbital Method as Cluster Expansion

      • Shigenori Tanaka

      Pages 3-14

   3. Comparison of Various Fragmentation Methods for Quantum Chemical Calculations of Large Molecular Systems

      • Shigenori Tanaka

      Pages 15-27

3. Programs

   1. Front Matter

      Pages 29-29

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   2. Recent Development of the Fragment Molecular Orbital Method in GAMESS

      • Dmitri G. Fedorov

      Pages 31-51

   3. The ABINIT-MP Program

      • Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato et al.

      Pages 53-67

   4. PAICS: Development of an Open-Source Software of Fragment Molecular Orbital Method for Biomolecule

      • Takeshi Ishikawa

      Pages 69-76

   5. Open-Architecture Program of Fragment Molecular Orbital Method for Massive Parallel Computing (OpenFMO) with GPU Acceleration

      • Hirotaka Kitoh-Nishioka, Hiroaki Umeda, Yasuteru Shigeta

      Pages 77-90

4. Pharmaceutical Activities

   1. Front Matter

      Pages 91-91

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   2. How to Perform FMO Calculation in Drug Discovery

      • Kaori Fukuzawa, Chiduru Watanabe, Yoshio Okiyama, Tatsuya Nakano

      Pages 93-125

   3. FMO Drug Design Consortium

      • Kaori Fukuzawa, Shigenori Tanaka, Yoichiro Yagi, Noriyuki Kurita, Norihito Kawashita, Kenichiro Takaba et al.

      Pages 127-181

   4. Development of an Automated FMO Calculation Protocol to Construction of FMO Database

      • Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya

      Pages 183-203

   5. Application of FMO to Ligand Design: SBDD, FBDD, and Protein–Protein Interaction

      • Tomonaga Ozawa, Motoyasu Ozawa

      Pages 205-251

   6. Drug Discovery Screening by Combination of X-ray Crystal Structure Analysis and FMO Calculation

      • Midori Takimoto-Kamimura, Noriyuki Kurita

      Pages 253-265

   7. Cooperative Study Combining X-ray Crystal Structure Analysis and FMO Calculation: Interaction Analysis of FABP4 Inhibitors

      • Uno Tagami, Kazutoshi Takahashi

      Pages 267-279

   8. Application of FMO for Protein–ligand Binding Affinity Prediction

      • Kenichiro Takaba

      Pages 281-294

   9. Recent Advances of In Silico Drug Discovery: Integrated Systems of Informatics and Simulation

      • Teruki Honma

      Pages 295-306

   10. Pharmaceutical Industry—Academia Cooperation

       • Alexander Heifetz, Peter V. Coveney, Dmitri G. Fedorov, Inaki Morao, Tim James, Michelle Southey et al.

       Pages 307-322

   11. Elucidating the Efficacy of Clinical Drugs Using FMO

       • Sundaram Arulmozhiraja, Hiroaki Tokiwa, Hitoshi Shimano

       Pages 323-339

This book covers recent advances of the fragment molecular orbital (FMO) method, consisting of 5 parts and a total of 30 chapters written by FMO experts. The FMO method is a promising way to calculate large-scale molecular systems such as proteins in a quantum mechanical framework. The highly efficient parallelism deserves being considered the principal advantage of FMO calculations. Additionally, the FMO method can be employed as an analysis tool by using the inter-fragment (pairwise) interaction energies, among others, and this feature has been utilized well in biophysical and pharmaceutical chemistry. In recent years, the methodological developments of FMO have been remarkable, and both reliability and applicability have been enhanced, in particular, for non-bio problems. The current trend of the parallel computing facility is of the many-core type, and adaptation to modern computer environments has been explored as well. In this book, a historical review of FMO and comparison to other methods are provided in Part I (two chapters) and major FMO programs (GAMESS-US, ABINIT-MP, PAICS and OpenFMO) are described in Part II (four chapters). dedicated to pharmaceutical activities (twelve chapters). A variety of new applications with methodological breakthroughs are introduced in Part IV (six chapters). Finally, computer and information science-oriented topics including massively parallel computation and machine learning are addressed in Part V (six chapters). Many color figures and illustrations are included. Readers can refer to this book in its entirety as a practical textbook of the FMO method or read only the chapters of greatest interest to them.

• Fragment molecular orbital
• FMO
• Parallel computation
• Interaction analyses
• Structure based drug design

• Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo, Japan

  Yuji Mochizuki

• Graduate School of System Informatics, Kobe University, Kobe, Japan

  Shigenori Tanaka

• School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan

  Kaori Fukuzawa

Yuji Mochizuki, Dr. Sci., Professor, Rikkyo University


Yuji Mochizuki received his Ph.D. degree in quantum chemistry in 1990 from Hokkaido University. He worked at the NEC Corporation (1990–1997) and Japan
Atomic Energy Research Institute (1997–2003). Then, he started the code development works and related applications of the FMO method with the
ABINIT-MP program at the University of Tokyo (2003–2006). Currently, he is a Professor of chemistry at Rikkyo University. His research interests are spread over multiscale simulations, machine-learning analyses of calculated results, and high-performance computing, besides the development of ABINIT-MP.


Shigenori Tanaka, Dr. Sci., Professor, Kobe University


Shigenori Tanaka received his Ph.D. in theoretical physics in 1986 from the University of Tokyo. He worked as a Research Associate at the University of Tokyo and later as a Researcher at the Toshiba Research and Development Center. Meanwhile, he worked at the California Institute of Technology in 1995–1996 as a Visiting Researcher. Since 2004, he has been a Professor at Kobe University. His primary research interests are the development of first-principles computational methods for biomolecular systems and their applications for bottom-up modeling of biological phenomena.


Kaori Fukuzawa, Dr. Eng., Associate Professor, Hoshi University


Kaori Fukuzawa received her M.S. in quantum chemistry from Rikkyo University in 1997 and Ph.D. in applied quantum chemistry from the University of Tokyo in 2001. She worked at the Mizuho Information and Research Institute (2000–2014) and Nihon University (2014–2016). She has been an Associate Professor at Hoshi University since 2016. Her research interests include application of quantum chemistry for in silico drug discovery, computational structural biology, and understanding chemical phenomena of biomolecular systems.

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