| Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations J Jung, W Nishima, M Daniels, G Bascom, C Kobayashi, A Adedoyin, ... Journal of computational chemistry 40 (21), 1919-1930, 2019 | 119 | 2019 |
| Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-glycans in solution W Nishima, N Miyashita, Y Yamaguchi, Y Sugita, S Re The Journal of Physical Chemistry B 116 (29), 8504-8512, 2012 | 90 | 2012 |
| Mosaic of water orientation structures at a neutral zwitterionic lipid/water interface revealed by molecular dynamics simulations S Re, W Nishima, T Tahara, Y Sugita The journal of physical chemistry letters 5 (24), 4343-4348, 2014 | 68 | 2014 |
| Confident identification of isomeric N‐glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography Y Yamaguchi, W Nishima, S Re, Y Sugita Rapid Communications in Mass Spectrometry 26 (24), 2877-2884, 2012 | 67 | 2012 |
| Conformational flexibility of N-glycans in solution studied by REMD simulations S Re, W Nishima, N Miyashita, Y Sugita Biophysical reviews 4, 179-187, 2012 | 46 | 2012 |
| Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing W Nishima, S Kanamaru, F Arisaka, A Kitao Journal of the American Chemical Society 133 (34), 13571-13576, 2011 | 27 | 2011 |
| Characterization of conformational ensembles of protonated N-glycans in the gas-phase S Re, S Watabe, W Nishima, E Muneyuki, Y Yamaguchi, AD MacKerell Jr, ... Scientific Reports 8 (1), 1644, 2018 | 26 | 2018 |
| Mechanisms for two-step proton transfer reactions in the outward-facing form of MATE transporter W Nishima, W Mizukami, Y Tanaka, R Ishitani, O Nureki, Y Sugita Biophysical Journal 110 (6), 1346-1354, 2016 | 19 | 2016 |
| Backbone circularization coupled with optimization of connecting segment in effectively improving the stability of granulocyte-colony stimulating factor T Miyafusa, R Shibuya, W Nishima, R Ohara, C Yoshida, S Honda ACS Chemical Biology 12 (10), 2690-2696, 2017 | 18 | 2017 |
| Water orientation at ceramide/water interfaces studied by heterodyne-detected vibrational sum frequency generation spectroscopy and molecular dynamics simulation A Adhikari, S Re, W Nishima, M Ahmed, S Nihonyanagi, JB Klauda, ... The Journal of Physical Chemistry C 120 (41), 23692-23697, 2016 | 18 | 2016 |
| DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins W Nishima, G Qi, S Hayward, A Kitao Bioinformatics 25 (5), 628-635, 2009 | 18 | 2009 |
| Full-length computational model of the SARS-CoV-2 spike protein and its implications for a viral membrane fusion mechanism W Nishima, M Kulik Viruses 13 (6), 1126, 2021 | 9 | 2021 |
| Structural transition and antibody binding of EBOV GP and ZIKV E proteins from pre-fusion to fusion-initiation state A Lappala, W Nishima, J Miner, P Fenimore, W Fischer, P Hraber, ... Biomolecules 8 (2), 25, 2018 | 9 | 2018 |
| Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting W Nishima, D Girodat, M Holm, EJ Rundlet, JL Alejo, K Fischer, ... Nucleic acids research 50 (14), 8302-8320, 2022 | 5 | 2022 |
| Correction to “Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations” S Re, W Nishima, T Tahara, Y Sugita The Journal of Physical Chemistry Letters 6 (1), 195-195, 2015 | 2 | 2015 |
| Drug extrusion process of mate multidrug efflux transporter revealed by molecular dynamics simulations W Nishima, Y Tanaka, R Ishitani, O Nureki, Y Sugita Biophysical Journal 106 (2), 801a, 2014 | 1 | 2014 |
| Ribosome hyper-swivel head domain motions are required for translocation and resetting DJ Girodat, W Nishima, M Holm, EJ Rundlet, JD Prajapati, JLA Amaya, ... Biophysical journal 122 (3), 360a, 2023 | | 2023 |
| Full-Length Computational Model of the SARS-CoV-2 Spike Protein and Its Implications for a Viral Membrane Fusion Mechanism. Viruses 2021, 13, 1126 W Nishima, M Kulik s Note: MDPI stays neutral with regard to jurisdictional claims in published …, 2021 | | 2021 |
| Structural transition and antibody binding of Ebola GP and Zika E proteins from pre-fusion to fusion-initiation states A Lappala-Vernon, W Nishima, JC Miner, PW Fenimore, W Fischer, ... bioRxiv, 285130, 2018 | | 2018 |
| Exaggerated Swivel Motions of the Small Subunit Head Domain are Required for tRNA Translocation through the Bacterial Ribosome W Nishima, SC Blanchard, KY Sanbonmatsu Biophysical Journal 114 (3), 437a, 2018 | | 2018 |
