Daron M. Standley

Daron M. Standley Professor standley [at] biken.osaka-u.ac.jp


Ph.D. Chemistry, Columbia University, New York - 1998

BS Physics, Harvey Mudd College, Claremont, CA - 1993

Research & Career

Guest Associate Professor, Center for Advanced Medical Engineering and Informatics, Institute for Protein Research, Osaka University (April, 2006 to September, 2008)

Senior Researcher, Protein Data Bank Japan, Institute for Protein Research, Osaka University (April, 2003 to September, 2008)

Scientific Software Developer Schrödinger, Inc. (September, 1998 to March, 2003)


Prize for Outstanding Achievement in Education and Research at Osaka University in 2009


Year Authors Title Publication Cites
2013 K Katoh, DM Standley MAFFT multiple sequence alignment software version 7: improvements in performance and usability MOLECULAR BIOLOGY AND EVOLUTION, 2013 34372
2022 T Arimori, N Ikemura, T Okamoto, J Takagi… Engineering ACE2 decoy receptors to combat viral escapability TRENDS IN …, 2022 26
2010 T Satoh, O Takeuchi, A Vandenbon, K Yasuda… The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection NATURE …, 2010 1205
2009 K Matsushita, O Takeuchi, DM Standley, Y Kumagai… Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay NATURE, 2009 683
2019 J Rozewicki, S Li, KM Amada, DM Standley… MAFFT-DASH: integrated protein sequence and structural alignment NUCLEIC ACIDS …, 2019 561
2023 IT Desta, S Kotelnikov, G Jones, U Ghani, M Abyzov… The ClusPro AbEMap web server for the prediction of antibody epitopes NATURE PROTOCOLS, 2023 2
2021 Y Liu, WT Soh, J Kishikawa, M Hirose, EE Nakayama… An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies CELL, 2021 221
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016 489
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014 460
2013 T Uehata, H Iwasaki, A Vandenbon, K Matsushita… Malt1-induced cleavage of regnase-1 in CD4+ helper T cells regulates immune activation CELL, 2013 355
2015 T Mino, Y Murakawa, A Fukao, A Vandenbon… Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms CELL, 2015 354
2011 A Kitamura, Y Maekawa, H Uehara… A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans THE JOURNAL OF …, 2011 319
2009 M Yamamoto, DM Standley, S Takashima… A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 JOURNAL OF EXPERIMENTAL …, 2009 302
2011 H Iwasaki, O Takeuchi, S Teraguchi, K Matsushita… The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1 NATURE …, 2011 293
2020 AA Koesoema, DM Standley, T Senda… Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications APPLIED MICROBIOLOGY AND …, 2020 48
2021 N Singh, NV Frey, B Engels, DM Barrett, O Shestova… Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells NATURE MEDICINE, 2021 103
2010 S Liang, D Zheng, DM Standley, B Yao, M Zacharias… EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results BMC …, 2010 186
2014 N Takemura, T Kawasaki, J Kunisawa, S Sato… Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome NATURE …, 2014 156
2022 N Ikemura, S Taminishi, T Inaba, T Arimori… An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo SCIENCE TRANSLATIONAL …, 2022 35
2017 KK Nyati, K Masuda, MMU Zaman… TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a NUCLEIC ACIDS …, 2017 153
2012 AR Kinjo, H Suzuki, R Yamashita… Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format NUCLEIC ACIDS …, 2012 160
2023 S Kawamoto, K Uemura, N Hori, L Takayasu… Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota NATURE CELL …, 2023 11
2011 SJ Fleishman, TA Whitehead, EM Strauch… Community-wide assessment of protein-interface modeling suggests improvements to design methodology JOURNAL OF MOLECULAR …, 2011 156
2014 H Morikawa, N Ohkura, A Vandenbon… Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation PROCEEDINGS OF THE …, 2014 141
2009 T Schwede, A Sali, B Honig, M Levitt, HM Berman… Outcome of a workshop on applications of protein models in biomedical research STRUCTURE, 2009 151
2016 K Masuda, B Ripley, KK Nyati, PK Dubey… Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA JOURNAL OF EXPERIMENTAL …, 2016 93
2014 S Tartey, K Matsushita, A Vandenbon, D Ori… Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex THE EMBO …, 2014 97
2013 R Moretti, SJ Fleishman, R Agius… Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions PROTEINS: STRUCTURE …, 2013 111
2017 M Sasai, N Sakaguchi, JS Ma, S Nakamura… Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense NATURE …, 2017 90
2023 Y Mitsui, T Suzuki, K Kuniyoshi, J Inamo, K Yamaguchi… Expression of the readthrough transcript CiDRE in alveolar macrophages boosts SARS-CoV-2 susceptibility and promotes COVID-19 severity IMMUNITY, 2023 4
2019 D Schritt, S Li, J Rozewicki, K Katoh… Repertoire Builder: high-throughput structural modeling of B and T cell receptors … SYSTEMS DESIGN & …, 2019 64
2022 A Tanaka, S Maeda, T Nomura… Construction of a T cell receptor signaling range for spontaneous development of autoimmune disease JOURNAL OF EXPERIMENTAL …, 2022 11
2019 D Yamasoba, K Sato, T Ichinose, T Imamura… N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation NATURE …, 2019 67
2017 R Yonehara, S Nada, T Nakai, M Nakai… Structural basis for the assembly of the Ragulator-Rag GTPase complex NATURE …, 2017 71
2012 K Maruyama, M Fukasaka, A Vandenbon, T Saitoh… The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation IMMUNITY, 2012 85
2015 M Onishi, K Ozasa, K Kobiyama, K Ohata… Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen THE JOURNAL OF …, 2015 71
2014 S Li, K Yamashita, KM Amada… Quantifying sequence and structural features of protein–RNA interactions NUCLEIC ACIDS …, 2014 67
2022 Z Xu, A Davila, J Wilamowski, S Teraguchi… Improved antibody‐specific epitope prediction using alphafold and abadapt …, 2022 21
2020 DS Saputri, S Li, FJ Van Eerden, J Rozewicki… Flexible, functional, and familiar: characteristics of SARS-CoV-2 spike protein evolution FRONTIERS IN …, 2020 39
2023 T Shirai, A Nakai, E Ando, J Fujimoto, S Leach… Celastrol suppresses humoral immune responses and autoimmunity by targeting the COMMD3/8 complex SCIENCE …, 2023 5
2019 T Mino, N Iwai, M Endo, K Inoue, K Akaki… Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs NUCLEIC ACIDS …, 2019 47
2014 K Yamashita, K Ikeda, K Amada, S Liang… Kotai Antibody Builder: automated high-resolution structural modeling of antibodies …, 2014 62
2020 K Fukushima, T Satoh, F Sugihara, Y Sato, T Okamoto… Dysregulated expression of the nuclear exosome targeting complex component Rbm7 in nonhematopoietic cells licenses the development of fibrosis IMMUNITY, 2020 36
2019 K Takeda, S Sakakibara, K Yamashita… Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis JOURNAL OF ALLERGY AND …, 2019 51
2011 S Liang, D Zheng, C Zhang, DM Standley Fast and accurate prediction of protein side-chain conformations BIOINFORMATICS, 2011 62
2013 Y Enokizono, H Kumeta, K Funami… Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling PROCEEDINGS OF THE …, 2013 68
2016 M Yokogawa, T Tsushima, NN Noda, H Kumeta… Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions SCIENTIFIC REPORTS, 2016 52
2018 H Hanieh, K Masuda, H Metwally… Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem‐loop structure in its 3′UTR EUROPEAN JOURNAL OF …, 2018 46
2014 H Shirai, K Ikeda, K Yamashita… High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations PROTEINS: STRUCTURE …, 2014 56
2017 M Hayashi, T Aoshi, Y Haseda, K Kobiyama… Advax, a delta inulin microparticle, potentiates in-built adjuvant property of co-administered vaccines …, 2017 44
2014 MF Lensink, IH Moal, PA Bates… Blind prediction of interfacial water positions in CAPRI PROTEINS: STRUCTURE …, 2014 61
2006 HM Berman, SK Burley, W Chiu, A Sali, A Adzhubei… Outcome of a workshop on archiving structural models of biological macromolecules STRUCTURE, 2006 68
2020 H Metwally, T Tanaka, S Li, G Parajuli, S Kang… Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production SCIENCE …, 2020 29
2022 A Davila, Z Xu, S Li, J Rozewicki… AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence BIOINFORMATICS …, 2022 18
2020 Y Lee, H Yamada, A Pradipta, JS Ma… Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense LIFE SCIENCE …, 2020 27
2020 S Teraguchi, DS Saputri… Methods for sequence and structural analysis of B and T cell receptor repertoires COMPUTATIONAL AND …, 2020 26
2023 IT Desta, S Kotelnikov, G Jones, U Ghani… Mapping of antibody epitopes based on docking and homology modeling PROTEINS: STRUCTURE …, 2023 6
2013 T Kawasaki, N Takemura, DM Standley, S Akira… The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling CELL HOST & …, 2013 47
2010 T Katayama, K Arakawa, M Nakao, K Ono… The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows JOURNAL OF BIOMEDICAL …, 2010 54
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi… Various miRNAs compensate the role of miR-122 on HCV replication PLOS …, 2020 18
2007 DM Standley, H Toh, H Nakamura ASH structure alignment package: sensitivity and selectivity in domain classification BMC BIOINFORMATICS, 2007 53
2021 Y Liu, N Arase, J Kishikawa, M Hirose, S Li, A Tada… The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines BIORXIV, 2021 29
2011 S Liang, Y Zhou, N Grishin… Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions JOURNAL OF COMPUTATIONAL …, 2011 41
2008 DM Standley, AR Kinjo, K Kinoshita… Protein structure databases with new web services for structural biology and biomedical research BRIEFINGS IN …, 2008 53
2023 DS Saputri, HS Ismanto, DK Nugraha, Z Xu… Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences MSYSTEMS, 2023 1
2011 YH Lee, T Ikegami, DM Standley, K Sakurai… Binding Energetics of Ferredoxin‐NADP+ Reductase with Ferredoxin and Its Relation to Function …, 2011 37
2016 T Kouwaki, T Okamoto, A Ito, Y Sugiyama… Hepatocyte factor JMJD5 regulates hepatitis B virus replication through interaction with HBx JOURNAL OF …, 2016 30
2021 J Hirano, S Yoshio, Y Sakai… Hepatitis C virus modulates signal peptide peptidase to alter host protein processing PROCEEDINGS OF THE …, 2021 9
2017 S Sakakibara, T Arimori, K Yamashita, H Jinzai… Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus SCIENTIFIC REPORTS, 2017 28
2011 M Fernandez, Y Kumagai, DM Standley, A Sarai… Prediction of dinucleotide-specific RNA-binding sites in proteins BMC BIOINFORMATICS, 2011 41
2022 YK Chong, S Tartey, Y Yoshikawa, K Imami, S Li… Cyclin J–CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism SCIENCE …, 2022 4
2022 HS Ismanto, Z Xu, DS Saputri, J Wilamowski… Landscape of infection enhancing antibodies in COVID-19 and healthy donors COMPUTATIONAL AND …, 2022 8
1999 VA Eyrich, DM Standley, AK Felts… Protein tertiary structure prediction using a branch and bound algorithm PROTEINS: STRUCTURE …, 1999 77
2021 N Ikemura, S Taminishi, T Inaba, T Arimori, D Motooka… Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant BIORXIV, 2021 10
2012 A Vandenbon, S Teraguchi, S Akira… Systems biology approaches to toll‐like receptor signaling … SYSTEMS BIOLOGY AND …, 2012 34
2014 Y Furukawa, S Teraguchi, T Ikegami, O Dagliyan… Intrinsic disorder mediates cooperative signal transduction in STIM1 JOURNAL OF MOLECULAR …, 2014 29
2022 Z Xu, HS Ismanto, H Zhou, DS Saputri… Advances in antibody discovery from human BCR repertoires FRONTIERS IN …, 2022 3
2024 T Uehata, S Yamada, D Ori, A Vandenbon, A Giladi… Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz BLOOD, 2024 2
2015 J Ohshima, M Sasai, J Liu… RabGDIα is a negative regulator of interferon-γ–inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii PROCEEDINGS OF THE …, 2015 27
2016 Y Kamikawa, Y Hori, K Yamashita, L Jin… Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins CHEMICAL …, 2016 25
2020 AA Koesoema, DM Standley, S Ohshima, M Tamura… Control of enantioselectivity in the enzymatic reduction of halogenated acetophenone analogs by substituent positions and sizes TETRAHEDRON LETTERS, 2020 15
2011 M Lis, T Kim, JJ Sarmiento, D Kuroda… Bridging the gap between single-template and fragment based protein structure modeling using Spanner IMMUNOME …, 2011 27
2004 DM Standley, H Toh… Detecting local structural similarity in proteins by maximizing number of equivalent residues … : STRUCTURE, FUNCTION, AND …, 2004 38
1999 VA Eyrich, DM Standley, RA Friesner Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set JOURNAL OF MOLECULAR BIOLOGY, 1999 79
2023 A Millius, RG Yamada, H Fujishima… Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep PROCEEDINGS OF THE …, 2023 1
2005 DM Standley, H Toh, H Nakamura GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures BMC BIOINFORMATICS, 2005 36
2013 AJ Hobro, DM Standley, S Ahmad… Deconstructing RNA: optical measurement of composition and structure PHYSICAL CHEMISTRY …, 2013 24
2019 S Li, J Wilamowski, S Teraguchi, FJ van Eerden… Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF …, 2019 13
2008 K Hamblin, DM Standley, MB Rogers… Localization and nucleotide specificity of Blastocystis succinyl‐CoA synthetase MOLECULAR …, 2008 31
2022 DM Standley, T Nakanishi, Z Xu, S Haruna, S Li… The evolution of structural genomics BIOPHYSICAL …, 2022 2
2013 S Liang, D Zheng, DM Standley, H Guo, C Zhang A novel function prediction approach using protein overlap networks BMC SYSTEMS BIOLOGY, 2013 23
1999 DM Standley, VA Eyrich, AK Felts, RA Friesner… A branch and bound algorithm for protein structure refinement from sparse NMR data sets JOURNAL OF MOLECULAR …, 1999 50
2019 AA Koesoema, Y Sugiyama, Z Xu, DM Standley… Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain APPLIED MICROBIOLOGY …, 2019 15
2006 P Gou, GT Hanke, Y Kimata-Ariga, DM Standley… Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins BIOCHEMISTRY, 2006 32
2019 AA Koesoema, Y Sugiyama, KT Sriwong, Z Xu… Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction APPLIED MICROBIOLOGY …, 2019 14
2007 E Kanamori, Y Murakami, Y Tsuchiya… Docking of protein molecular surfaces with evolutionary trace analysis PROTEINS: STRUCTURE …, 2007 33
2012 S Liang, C Zhang, J Sarmiento… Protein loop modeling with optimized backbone potential functions JOURNAL OF CHEMICAL …, 2012 19
2019 Z Xu, S Li, J Rozewicki, K Yamashita… Functional clustering of B cell receptors using sequence and structural features … SYSTEMS DESIGN & …, 2019 11
2021 K Katoh, DM Standley Emerging SARS-CoV-2 variants follow a historical pattern recorded in outgroups infecting non-human hosts COMMUNICATIONS BIOLOGY, 2021 5
2022 H Monhemi, HN Hoang, DM Standley… The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions PHYSICAL CHEMISTRY …, 2022 2
2022 Y Mitsui, T Suzuki, K Kuniyoshi, J Inamo, K Yamaguchi… CiDRE+ M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity BIORXIV, 2022 3
2023 T Lusiany, T Terada, J Kishikawa, M Hirose, DV Chen… Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies VIRUSES, 2023 0
2009 R Apostolov, Y Yonezawa, DM Standley… Membrane attachment facilitates ligand access to the active site in monoamine oxidase A BIOCHEMISTRY, 2009 19
2011 J Ikebe, DM Standley, H Nakamura, J Higo Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster PROTEIN SCIENCE, 2011 25
2022 Y Saijo-Hamano, AA Sherif, A Pradipta… Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6 LIFE SCIENCE …, 2022 8
2020 Y Liu, WT Soh, A Tada, A Arakawa, S Matsuoka… An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies BIORXIV, 2020 9
2022 S Beppu, M Kinoshita, J Wilamowski, T Suenaga… High cell surface expression and peptide binding affinity of HLA-DQA1*05:03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD) SCIENTIFIC REPORTS, 2022 3
2019 H Fukuda, S Li, L Sardo, JL Smith… Structural determinants of the APOBEC3G N-terminal domain for HIV-1 RNA association FRONTIERS IN CELLULAR …, 2019 11
2015 D Hall, S Li, K Yamashita, R Azuma, JA Carver… RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure ANALYTICAL …, 2015 14
2020 AA Koesoema, DM Standley, M Tamura, T Matsuda Access to both enantiomers of substituted 2-tetralol analogs by a highly enantioselective reductase TETRAHEDRON LETTERS, 2020 11
2022 M Loza, S Teraguchi, DM Standley… Unbiased integration of single cell transcriptome replicates NAR GENOMICS AND …, 2022 6
1998 DM Standley, JR Gunn, RA Friesner… Tertiary structure prediction of mixed α/β proteins via energy minimization PROTEINS: STRUCTURE …, 1998 38
2023 FJ van Eerden, AA Sherif, MA Llamas-Covarrubias… TCR-pMHC complex formation triggers CD3 dynamics ELIFE, 2023 1
2017 J Hirano, T Okamoto, Y Sugiyama… Characterization of SPP inhibitors suppressing propagation of HCV and protozoa PROCEEDINGS OF THE …, 2017 10
2012 A Vandenbon, Y Kumagai, S Akira, DM Standley A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription BMC GENOMICS, 2012 13
2001 DM Standley, VA Eyrich, Y An… Protein structure prediction using a combination of sequence‐based alignment, constrained energy minimization, and structural alignment PROTEINS: STRUCTURE …, 2001 23
2010 S Teraguchi, A Patil, DM Standley Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins BMC BIOINFORMATICS, 2010 13
2010 DM Standley, R Yamashita, AR Kinjo, H Toh… SeSAW: balancing sequence and structural information in protein functional mapping …, 2010 14
2023 N Jiravejchakul, GL Abe, M Loza, S Park… Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine BMC GENOMICS, 2023 0
2023 YD Kuan, CY Tsai, S Sakakibara, DM Standley… External stimulation induces the secretion of autophagosome-like vesicles by B cells AUTOPHAGY …, 2023 1
2012 A Patil, S Teraguchi, H Dinh, K Nakai… Functional annotation of intrinsically disordered domains by their amino acid content using IDD navigator BIOCOMPUTING …, 2012 9
2008 DM Standley, H Toh… Functional annotation by sequence‐weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan … : STRUCTURE, FUNCTION, AND …, 2008 11
2010 RJ Milewski, Y Kumagai, K Fujita, DM Standley… Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis IMMUNOME …, 2010 9
2011 S Liang, C Zhang, DM Standley Protein loop selection using orientation‐dependent force fields derived by parameter optimization PROTEINS: STRUCTURE, FUNCTION …, 2011 8
2011 S Teraguchi, Y Kumagai, A Vandenbon, S Akira… Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations PHYSICAL REVIEW E, 2011 9
2017 B Nosirov, J Billaud, A Vandenbon, D Diez… Mapping circulating serum miRNAs to their immune-related target mRNAs … AND APPLICATIONS IN …, 2017 6
2024 MA Llamas-Covarrubias, A Tanaka, MJ Loza Lopez… Th17 cells with a pathogenic signature in joints of ZAP-70 mutant arthritic mice harbor unique TCR repertoires that share features with WT Tregs BIORXIV, 2024 0
2006 DM Standley, Y Yonezawa, Y Goto, H Nakamura Flexible docking of an amyloid-forming peptide from β2-microglobulin FEBS LETTERS, 2006 8
2014 D Hall, S Li, K Yamashita, R Azuma, JA Carver… A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein BIOPHYSICAL …, 2014 5
2024 H Okuma, Y Saijo‐Hamano, H Yamada… Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I GENES TO …, 2024 0
2023 Z Xu, HS Ismanto, DS Saputri, S Haruna, G Sun… Robust diagnosis of infectious disease, autoimmunity and cancer from the paratope networks of adaptive immune receptors BIORXIV, 2023 0
2002 VA Eyrich, RA Friesner… Ab Initio Protein Structure Prediction Using a Size‐dependent Tertiary Folding Potential … METHODS FOR PROTEIN …, 2002 7
2012 DM Standley, M van der Giezen Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly RESEARCH AND REPORTS IN …, 2012 5
2022 J Wilamowski, Z Xu, HS Ismanto, S Li, S Teraguchi… InterClone: Store, search and cluster Adaptive immune receptor repertoires BIORXIV, 2022 2
2023 S Taminishi, S Li, Y Higuchi, Y Kirita, D Motooka… Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system BIORXIV, 2023 0
2014 A Vandenbon, S Teraguchi, O Takeuchi, Y Suzuki… Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation BMC GENOMICS, 2014 3
2021 J Rozewicki, S Li, K Katoh, DM Standley Analysis of protein intermolecular interactions with MAFFT-DASH MULTIPLE SEQUENCE ALIGNMENT …, 2021 1
2022 FJ van Eerden, AA Sherif, MA Llamas-Covarrubias… TCR binding to peptide-MHC complex acts as a drawbridge for CD3 cross-membrane signaling BIORXIV, 2022 0
2022 K Stapleton, T Mizobata, N Miyazaki, T Takatsuji… Three-dimensional motions of GroEL during substrate protein recognition BIORXIV, 2022 0
2022 T Lusiany, Z Xu, DS Saputri, HS Ismanto… Structural Modeling of Adaptive Immune Responses to Infection … -AIDED ANTIBODY DESIGN, 2022 0
2011 Y Yonezawa, DM Standley, H Nakamura Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide CHEMICAL PHYSICS LETTERS, 2011 3
2013 A Vandenbon, Y Kumagai, S Teraguchi, KM Amada… A Parzen window-based approach for the detection of locally enriched transcription factor binding sites BMC …, 2013 3
2023 FJ van Eerden, AA Sherif, MA Llamas-Covarrubias… When the TCR's engaged, the CD3 epsilons will play: A dynamic T cell receptor (TCR) triggering mechanism BIOPHYSICAL …, 2023 0
2013 DM Standley, K Katoh MAFFT multiple sequence alignment software version 7: improvements in performance and usability MOLECULAR BIOLOGY AND EVOLUTION, 2013 282
2011 AR Kinjo, Y Kumagai, H Dinh, O Takeuchi… Functional characterization of protein domains common to animal viruses and mouse BMC GENOMICS, 2011 2
2008 DM Standley, AR Kinjo, M Lis, M van der Giezen… Structure-based functional annotation of protein sequences guided by comparative models … ON OPTIMIZATION AND …, 2008 1
2022 D Standley An adaptive approach to predicting antibody-antigen complex structures from sequence BIOPHYSICAL JOURNAL, 2022 0
2013 E Kanamori, Y Murakami, J Sarmiento… Prediction of protein-protein complex structures … FORMS AND FUNCTIONS …, 2013 1
2019 AA Koesoema, Y Sugiyama, Z Xu… Correction to: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain APPLIED …, 2019 1
2002 AR Dinner, SS So, M Karplus, D Thirumalai, DK Klimov… Computational Methods for Protein Folding , 2002 1
2021 H Arase, Y Liu, N Arase, J Kishikawa, M Hirose, S Li… Acquisition of resistance to wild-type spike-immune sera by emerging SARS-CoV-2 variants , 2021 0
2021 K Katoh, DM Standley A simple method for predicting emerging SARS-CoV-2 variants using outgroups infecting non-human hosts , 2021 0
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi… Various miRNAs are involved in efficient HCV replication BIORXIV, 2020 0
2023 S Taminishi, S Li, Y Higuchi, Y Kirita, D Motooka… Deep mutational scanning of whole SARS-CoV-2 spike in an inverted infection system (preprint) , 2023 0
1998 DM Standley Protein tertiary structure prediction by constrained and unconstrained energy minimization , 1998 0
2019 DM Standley, JDO Nieri, S Li, D Schritt… Immunological entity clustering software US PATENT APP. 16 …, 2019 0
2007 DM Standley, H Toh, H Nakamura S08I2 Functional Annotation Sequence-weighted Structure Alignments (Bioinformatics in the Era of Structural Proteomics) SEIBUTSU BUTSURI, 2007 0
2022 DM Standley Molecular mechanism of SARS-CoV-2 infection-enhancing antibodies PROGRAM&ABSTRACT BOOK プログラム・抄録集, 2022 0
2022 HS Ismanto, Z Xu, DS Saputri, J Wilamowski, S Li… Landscape of infection enhancing antibodies in COVID-19 and healthy donors (preprint) , 2022 0
2000 VA Eyrich, DM Standley, RA Friesner Global Optimization and Sampling in the Context of Tertiary Structure Prediction: A Comparison of Two Algorithms OPTIMIZATION IN COMPUTATIONAL …, 2000 0
2022 Y Mitsui, T Suzuki, K Kuniyoshi, J Inamo, K Yamaguchi… CiDRE+ M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity (preprint) , 2022 0
2017 D Schritt, K Katoh, S Li, DM Standley Modeling Biocatalysts FUTURE DIRECTIONS IN BIOCATALYSIS, 2017 0
2022 Z Xu, HS Ismanto, S Li, S Teraguchi, MAL Covarrubias… InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires (preprint) , 2022 0
2010 K Oshima, D Standley, E Kanamori, Y Murakami… 3P294 Structural modeling for protein complexes using small angle x-ray scattering (Bioinformatics: Structural genomics, The 48th Annual Meeting of the Biophysical … SEIBUTSU …, 2010 0
2020 Y Liu, WT Soh, A Tada, A Arakawa, S Matsuoka… An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies (preprint) , 2020 0
2006 DM Standley, H Toh, H Nakamura 1P481 Real-time Structure Based Queries at the Protein Data Bank japan (23. Bioinformatics, genomics and proteomics (I), Poster Session, Abstract, Meeting Program … SEIBUTSU BUTSURI, 2006 0
2021 N Ikemura, S Taminishi, T Inaba, T Arimori, D Motooka… Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant (preprint) , 2021 0
2020 AJ Wilk, MJ Lee, B Wei, B Parks, R Pi… Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19 (preprint) , 2020 0
2021 Y Liu, N Arase, J Kishikawa, M Hirose, S Li, A Tada… The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines (preprint) , 2021 0
2009 DM Standley, M Lis, AR Kinjo, H Nakamura Protein Function Annotation from Sequences and Structures with Tools at PDBj 亚洲晶体学联合大会摘要集, 2009 0
2020 KM Ji, L Ji-eun, CJ Keun, P Jungwook, J Jin, Y Ji-eun… Genomic and phylogenetic analyses of SARS-CoV-2 strains isolated in the city of Gwangju, South Korea (preprint) , 2020 0
2021 H Arase, Y Liu, N Arase, J Kishikawa, M Hirose, S Li… Acquisition of resistance to wild-type spike-immune sera by emerging SARS-CoV-2 variants (preprint) , 2021 0
2020 RNM Ghazzali, A Pain, M Abdollahyan, E Gadaleta… assayM: a web application to monitor mutations in COVID-19 diagnostic assays.(preprint) , 2020 0
2005 DM Standley, H Nakamura Beyond Text-based Queries at the Protein Data Bank, Japan ACTA CRYSTALLOGRAPHICA A …, 2005 0
2020 J Oscanoa, L Sivapalan, M Abdollahyan, E Gadaleta… SNPnexus COVID: Facilitating the analysis of COVID-19 host genetics (preprint) , 2020 0
2016 SK Suzuki, J Hirano, T Fukuhara, A Yamashita, K Saito… Hepatocyte factor JMJD5 regulates HBV replication through interaction with HBx , 2016 0
2008 DM Standley, H Nakamura From structures to functions: annotation by structural bioinformatics TANPAKUSHITSU KAKUSAN KOSO …, 2008 1
2008 DM Standley, AR Kinjo, H Nakamura Functional annotation by sequence-weighted structural alignments FOUNDATIONS OF …, 2008 0
2001 DM Standley, VA Eyrich, Y An… Ab Initio: Prediction Reports-Protein Structure Prediction Using a Combination of Sequence-Based Alignment, Constrained Energy Minimization, and … PROTEINS …, 2001 0
2012 E Kanamori, Y Tsuchiya… Prediction of Protein-Protein Complex Structures Using a Docking Server, surFit PROTEIN …, 2012 0
2019 AA Koesoema, Y Sugiyama… Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain (vol 47, pg 583 … APPLIED …, 2019 0
2008 Y Tsuchiya, E Kanamori, DM Standley… Development of a scoring method for predicting protein complex structures ACTA …, 2008 0
2005 H Nakamura, N Ito, R Yamashita… PDBML: the XML-based database and its applications ACTA …, 2005 0
2014 DM Standley 2SCP-07 Intrinsic disorder mediates cooperative signal transduction in STIM1 (構造バイオインフォマティクスによる蛋白質機能予測・解析, シンポジウム, 第 52 … 生物物理, 2014 0
2010 O Kanji, S Daron, K Eiji, M Yoichi, O Tomotaka… 3P294 X 線小角散乱を用いたタンパク質複合体の構造モデリング (生命情報科学-構造ゲノミクス, 第 48 回日本生物物理学会年会) 生物物理, 2010 0