Wataru Nishima

Postdoctoral Research Associate

About

Research Scientist. Has over 12 years of professional research experience including detail-oriented computational design of cytokine/enzyme with Rosetta framework (Protein design, Ab initio/homology/loop modeling, Sequence/structural analysis, Statistical analysis). Investigated biological phenomenon and proposed mechanism in the context of SARS-CoV-2, T4-phage infection, Ebola/Zika virus prefusion-fusion transition, multi-drug resistance, GATA4 human gene with MD, and QM/MM simulations. Developed methodologies such as characterization of complex N-glycan conformation. Always led creative solutions to tackle challenging new/unresolved problems with unique ideas/analysis and solid advanced computation skills (Parallel computing / Database) including the experience of massive computing usage (>100,000 cpu cores).

Country

Japan

City

Osaka

Industry

Research

Skill

Computational Biology, Bioinformatics, Molecular Dynamics, Molecular Biology, Numerical Analysis, Statistical Data Analysis, Data Analysis, Web Applications, Statistical Analysis, Research, Statistics, Databases, QM/MM, Drug Design, Protein Design, Computational Physics, Computational Chemistry, Biophysics, Parallel Computing, Scientific Computing

Experience

Postdoctoral Research Associate

National institute of Biomedical Innovation, Health, Nutrition

2024-3 - Present · 2 yrs 7 mos

Osaka, Japan

https://archer.nibiohn.go.jp/en/organization/insilico

Director of Protein Design

Proselbiosciences

2021-8 - 2021-12 · 5 mos

Santa Fe, New Mexico, United States

For details https://proselbio.com/

Bioinformatics Scientist

Spartina Biotechnologies

2020-8 - 2021-12 · 1 yr 5 mos

Working on the antiviral drug development for COVID-19 (RNA structural modeling and design collaborating with LANL).

Research Scientist

New Mexico Consortium

2016-9 - 2021-12 · 5 yrs 4 mos

Los Alamos, NM, USA

Working on USDA (US Department of Agriculture) project Will work on COVID19 therapeutics research

Scientist (Protein design)

Arzeda

2019-3 - 2020-7 · 1 yr 5 mos

Seattle, WA

-enzyme design using Rosetta and co-evolutionary approach

Visiting Scientist

Los Alamos National Laboratory

2016-9 - 2020-3 · 3 yrs 7 mos

Los Alamos, New Mexico, United States

- Assembled human GATA4 gene model (>1 Billon atoms) and delivered world the largest MD simulation with over 500,000 cores (corresponding to whole nodes) of Trinity supercomputer at Los Alamos National Laboratory. Developed software to handle 1 billion atom system. - Modeled, characterized and performed MD simulation for an unresolved “super-swivel” state of the ribosome model suggested from Fluorescence Resonance Energy Transfer (FRET) constraints. - Constructed transition conformations from perfusion to fusion state of Zika/Ebola virus spike proteins.

Postdoctoral Researcher

RIKEN

2011-4 - 2016-7 · 5 yrs 4 mos

Japan

- Elucidated the export mechanism of multidrug transporter MATE. Proposed a model of proton transfer that drives for drug extrusions causing multi-drug resistance. - Developed a methodology to characterize the complex conformation of N-glycan. Demonstrated the separation of collision cross-section (CCS) in Ion Mobility Mass Spectrometry (IM-MS) is attributed to distinct conformations of glycan. Proved the concept of IM-MS signal separation by glycosylic isomers.

Postdoctoral Researcher

National Institute of Advanced Industrial Science and Technology (AIST)

2009-9 - 2011-3 · 1 yr 7 mos

Japan

Successfully obtained an optimal sequence of the protein (cytokine) to improve the stability and function. The methodology for the backbone refinement was also developed based on protein design procedure such as DEE, FASTER, and Rosetta score function. The designed protein was experimentally confirmed to have the indented structural stability.

Postdoctoral Researcher

The University of Tokyo

2009-4 - 2009-7 · 4 mos

Japan

Elucidated molecular mechanism of the initial infection process of bacteriophage T4. Successfully simulated the process of puncturing membrane with needle protein gp5 by using all-atoms MD simulation (about 1,000,000 atoms system). The interaction between protein and lipids during membrane penetration process was elucidated.

Simulation Research Fellow

The University of Tokyo

2005-10 - 2009-3 · 3 yrs 6 mos

Japan

Biostatistics of protein motions based on main-chain dihedral angle changes. Originated from a discovery of phenomena “dihedral angle transition” toward the methodology for the characterization of protein motion. Successfully applied this method onto 459 protein pairs resulting new feature of protein motions.

System Engineer and Project manager

Panasonic Shikoku Electronics

2001 - 2003 · 2 yrs

Japan

-Provided to outsource for photo album website. Resulted in over a 100,000 gain in 100,000 new members.  -Managed on four developers team. (cell phone website version) Reduced working hours 80% with sophisticated programming design.