Daron M. Standley

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

Education

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)

Awards

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

Publications

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, 30, 772-780 24512
2010 T Satoh, O Takeuchi, A Vandenbon, K Yasuda, Y Tanaka, Y Kumagai, ... The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection NATURE IMMUNOLOGY, 2010, 11, 936-944 1052
2009 K Matsushita, O Takeuchi, DM Standley, Y Kumagai, T Kawagoe, ... Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay NATURE, 2009, 458, 1185-1190 575
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 366
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016, 32, 1933-1942 341
2013 T Uehata, H Iwasaki, A Vandenbon, K Matsushita, E Hernandez-Cuellar, ... Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation CELL, 2013, 153, 1036-1049 287
2011 A Kitamura, Y Maekawa, H Uehara, K Izumi, I Kawachi, M Nishizawa, ... A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans THE JOURNAL OF CLINICAL INVESTIGATION, 2011, 121, 4150-4160 276
2015 T Mino, Y Murakawa, A Fukao, A Vandenbon, HH Wessels, D Ori, ... Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms CELL, 2015, 161, 1058-1073 273
2009 M Yamamoto, DM Standley, S Takashima, H Saiga, M Okuyama, ... A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 JOURNAL OF EXPERIMENTAL MEDICINE, 2009, 206, 2747-2760 269
2019 J Rozewicki, S Li, KM Amada, DM Standley, K Katoh MAFFT-DASH: integrated protein sequence and structural alignment NUCLEIC ACIDS RESEARCH 47 (W1), W5-W, 2019, 10 257
2011 H Iwasaki, O Takeuchi, S Teraguchi, K Matsushita, T Uehata, K Kuniyoshi, ... The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1 NATURE IMMUNOLOGY, 2011, 12, 1167-1175 252
2011 SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Community-wide assessment of protein-interface modeling suggests improvements to design methodology JOURNAL OF MOLECULAR BIOLOGY, 2011, 414, 289-302 146
2010 S Liang, D Zheng, DM Standley, B Yao, M Zacharias, C Zhang EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results BMC BIOINFORMATICS, 2010, 11, 1-6 144
2012 AR Kinjo, H Suzuki, R Yamashita, Y Ikegawa, T Kudou, R Igarashi, ... Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format NUCLEIC ACIDS RESEARCH 40 (D1), D453-D, 2012, 460 137
2009 T Schwede, A Sali, B Honig, M Levitt, HM Berman, D Jones, SE Brenner, ... Outcome of a workshop on applications of protein models in biomedical research STRUCTURE, 2009, 17, 151-159 137
2014 N Takemura, T Kawasaki, J Kunisawa, S Sato, A Lamichhane, ... Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome NATURE COMMUNICATIONS, 2014, 5, 1-15 127
2021 Y Liu, WT Soh, J Kishikawa, M Hirose, EE Nakayama, S Li, M Sasai, ... An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies CELL 184 (13), 3452-3466., 2021, 18 116
2014 H Morikawa, N Ohkura, A Vandenbon, M Itoh, S Nagao-Sato, H Kawaji, ... Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2014, 111, 5289-5294 116
2017 KK Nyati, K Masuda, MMU Zaman, PK Dubey, D Millrine, JP Chalise, ... TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a NUCLEIC ACIDS RESEARCH, 2017, 45, 2687-2703 108
2013 R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2013, 81, 1980-1987 100
2014 S Tartey, K Matsushita, A Vandenbon, D Ori, T Imamura, T Mino, ... Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex THE EMBO JOURNAL, 2014, 33, 2332-2348 82
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, 288, 725-742 79
1999 VA Eyrich, DM Standley, AK Felts, RA Friesner Protein tertiary structure prediction using a branch and bound algorithm PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 1999, 35, 41-57 75
2016 K Masuda, B Ripley, KK Nyati, PK Dubey, MMU Zaman, H Hanieh, M Higa, ... Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA JOURNAL OF EXPERIMENTAL MEDICINE, 2016, 213, 605-619 72
2012 K Maruyama, M Fukasaka, A Vandenbon, T Saitoh, T Kawasaki, T Kondo, ... The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation IMMUNITY, 2012, 37, 1024-1036 71
2017 M Sasai, N Sakaguchi, JS Ma, S Nakamura, T Kawabata, H Bando, Y Lee, ... Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense NATURE IMMUNOLOGY, 2017, 18, 899-910 61
2006 HM Berman, SK Burley, W Chiu, A Sali, A Adzhubei, PE Bourne, ... Outcome of a workshop on archiving structural models of biological macromolecules STRUCTURE, 2006, 14, 1211-1217 60
2013 Y Enokizono, H Kumeta, K Funami, M Horiuchi, J Sarmiento, K Yamashita, ... Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2013, 110, 19908-19913 57
2014 MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, ... Blind prediction of interfacial water positions in CAPRI PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2014, 82, 620-632 56
2015 M Onishi, K Ozasa, K Kobiyama, K Ohata, M Kitano, K Taniguchi, ... Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen THE JOURNAL OF IMMUNOLOGY, 2015, 194, 2673-2682 54
2011 S Liang, D Zheng, C Zhang, DM Standley Fast and accurate prediction of protein side-chain conformations BIOINFORMATICS, 2011, 27, 2913-2914 51
2010 T Katayama, K Arakawa, M Nakao, K Ono, KF Aoki-Kinoshita, ... The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows JOURNAL OF BIOMEDICAL SEMANTICS, 2010, 1, 1-19 51
2007 DM Standley, H Toh, H Nakamura ASH structure alignment package: sensitivity and selectivity in domain classification BMC BIOINFORMATICS, 2007, 8, 1-8 50
2014 K Yamashita, K Ikeda, K Amada, S Liang, Y Tsuchiya, H Nakamura, ... Kotai Antibody Builder: automated high-resolution structural modeling of antibodies BIOINFORMATICS, 2014, 30, 3279-3280 49
2014 S Li, K Yamashita, KM Amada, DM Standley Quantifying sequence and structural features of protein–RNA interactions NUCLEIC ACIDS RESEARCH, 2014, 42, 10086-10098 49
1999 DM Standley, VA Eyrich, AK Felts, RA Friesner, AE McDermott A branch and bound algorithm for protein structure refinement from sparse NMR data sets JOURNAL OF MOLECULAR BIOLOGY, 1999, 285, 1691-1710 48
2008 DM Standley, AR Kinjo, K Kinoshita, H Nakamura Protein structure databases with new web services for structural biology and biomedical research BRIEFINGS IN BIOINFORMATICS, 2008, 9, 276-285 47
2017 R Yonehara, S Nada, T Nakai, M Nakai, A Kitamura, A Ogawa, ... Structural basis for the assembly of the Ragulator-Rag GTPase complex NATURE COMMUNICATIONS, 2017, 8, 1-11 46
2014 H Shirai, K Ikeda, K Yamashita, Y Tsuchiya, J Sarmiento, S Liang, ... High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2014, 82, 1624-1635 45
2013 T Kawasaki, N Takemura, DM Standley, S Akira, T Kawai The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling CELL HOST & MICROBE, 2013, 14, 148-158 41
2019 D Schritt, S Li, J Rozewicki, K Katoh, K Yamashita, W Volkmuth, G Cavet, ... Repertoire Builder: high-throughput structural modeling of B and T cell receptors MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 761-768 39
2016 M Yokogawa, T Tsushima, NN Noda, H Kumeta, Y Enokizono, ... Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions SCIENTIFIC REPORTS, 2016, 6, 1-10 39
1998 DM Standley, JR Gunn, RA Friesner, AE McDermott Tertiary structure prediction of mixed α/β proteins via energy minimization PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 1998, 33, 240-252 38
2019 D Yamasoba, K Sato, T Ichinose, T Imamura, L Koepke, S Joas, E Reith, ... N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation NATURE MICROBIOLOGY, 2019, 4, 1532-1544 37
2011 M Fernandez, Y Kumagai, DM Standley, A Sarai, K Mizuguchi, S Ahmad Prediction of dinucleotide-specific RNA-binding sites in proteins BMC BIOINFORMATICS, 2011, 12, 1-10 37
2004 DM Standley, H Toh, H Nakamura Detecting local structural similarity in proteins by maximizing number of equivalent residues PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2004, 57, 381-391 37
2017 M Hayashi, T Aoshi, Y Haseda, K Kobiyama, E Wijaya, N Nakatsu, ... Advax, a delta inulin microparticle, potentiates in-built adjuvant property of co-administered vaccines EBIOMEDICINE, 2017, 15, 127-136 36
2018 H Hanieh, K Masuda, H Metwally, JP Chalise, M Mohamed, KK Nyati, ... Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem‐loop structure in its 3′UTR EUROPEAN JOURNAL OF IMMUNOLOGY, 2018, 48, 593-604 35
2011 S Liang, Y Zhou, N Grishin, DM Standley Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions JOURNAL OF COMPUTATIONAL CHEMISTRY, 2011, 32, 1680-1686 35
2007 E Kanamori, Y Murakami, Y Tsuchiya, DM Standley, H Nakamura, ... Docking of protein molecular surfaces with evolutionary trace analysis PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2007, 69, 832-838 31
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, 6, 1-19 31
2012 A Vandenbon, S Teraguchi, S Akira, K Takeda, DM Standley Systems biology approaches to toll‐like receptor signaling WILEY INTERDISCIPLINARY REVIEWS: SYSTEMS BIOLOGY AND MEDICINE, 2012, 4, 497-507 30
2008 K Hamblin, DM Standley, MB Rogers, A Stechmann, AJ Roger, R Maytum, ... Localization and nucleotide specificity of Blastocystis succinyl‐CoA synthetase MOLECULAR MICROBIOLOGY, 2008, 68, 1395-1405 30
2006 P Gou, GT Hanke, Y Kimata-Ariga, DM Standley, A Kubo, I Taniguchi, ... Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins BIOCHEMISTRY, 2006, 45, 14389-14396 30
2019 K Takeda, S Sakakibara, K Yamashita, D Motooka, S Nakamura, ... Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 143 (3), 1163-1175., 2019, 15 29
2011 YH Lee, T Ikegami, DM Standley, K Sakurai, T Hase, Y Goto Binding Energetics of Ferredoxin‐NADP+ Reductase with Ferredoxin and Its Relation to Function CHEMBIOCHEM, 2011, 12, 2062-2070 29
2019 T Mino, N Iwai, M Endo, K Inoue, K Akaki, F Hia, T Uehata, T Emura, ... Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs NUCLEIC ACIDS RESEARCH, 2019, 47, 8838-8859 28
2021 N Singh, NV Frey, B Engels, DM Barrett, O Shestova, P Ravikumar, ... Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells NATURE MEDICINE, 2021, 27, 842-850 27
2015 J Ohshima, M Sasai, J Liu, K Yamashita, JS Ma, Y Lee, H Bando, ... RabGDIα is a negative regulator of interferon-γ–inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 112 (33), E4581-, 2015, 4590 25
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, 20, 187-196 25
2016 T Kouwaki, T Okamoto, A Ito, Y Sugiyama, K Yamashita, T Suzuki, ... Hepatocyte factor JMJD5 regulates hepatitis B virus replication through interaction with HBx JOURNAL OF VIROLOGY, 2016, 90, 3530-3542 24
2014 Y Furukawa, S Teraguchi, T Ikegami, O Dagliyan, L Jin, D Hall, ... Intrinsic disorder mediates cooperative signal transduction in STIM1 JOURNAL OF MOLECULAR BIOLOGY, 2014, 426, 2082-2097 24
2011 M Lis, T Kim, JJ Sarmiento, D Kuroda, HV Dinh, AR Kinjo, K Amada, ... Bridging the gap between single-template and fragment based protein structure modeling using Spanner IMMUNOME RESEARCH, 2011, 7, 1-1 23
2001 DM Standley, VA Eyrich, Y An, DL Pincus, JR Gunn, RA Friesner Protein structure prediction using a combination of sequence‐based alignment, constrained energy minimization, and structural alignment PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS 45 (S5), 2001, 133-139 23
2016 Y Kamikawa, Y Hori, K Yamashita, L Jin, S Hirayama, DM Standley, ... Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins CHEMICAL SCIENCE, 2016, 7, 308-314 22
2013 S Liang, D Zheng, DM Standley, H Guo, C Zhang A novel function prediction approach using protein overlap networks BMC SYSTEMS BIOLOGY, 2013, 7, 1-10 22
2020 DS Saputri, S Li, FJ Van Eerden, J Rozewicki, Z Xu, HS Ismanto, A Davila, ... Flexible, functional, and familiar: characteristics of SARS-CoV-2 spike protein evolution FRONTIERS IN MICROBIOLOGY, 2020, 11, 2112-2112 21
2013 AJ Hobro, DM Standley, S Ahmad, NI Smith Deconstructing RNA: optical measurement of composition and structure PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2013, 15, 13199-13208 21
2017 S Sakakibara, T Arimori, K Yamashita, H Jinzai, D Motooka, S Nakamura, ... Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus SCIENTIFIC REPORTS, 2017, 7, 1-14 20
2020 AA Koesoema, DM Standley, T Senda, T Matsuda Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2020, 104, 2897-2909 19
2021 Y Liu, N Arase, J Kishikawa, M Hirose, S Li, A Tada, S Matsuoka, ... The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines BIORXIV, 2021 18
2020 H Metwally, T Tanaka, S Li, G Parajuli, S Kang, H Hanieh, S Hashimoto, ... Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production SCIENCE SIGNALING 13 (624), EAAY, 2020, 574 18
2020 K Fukushima, T Satoh, F Sugihara, Y Sato, T Okamoto, Y Mitsui, S Yoshio, ... Dysregulated expression of the nuclear exosome targeting complex component Rbm7 in nonhematopoietic cells licenses the development of fibrosis IMMUNITY 52 (3), 542-556., 2020, 13 17
2009 R Apostolov, Y Yonezawa, DM Standley, G Kikugawa, Y Takano, ... Membrane attachment facilitates ligand access to the active site in monoamine oxidase A BIOCHEMISTRY, 2009, 48, 5864-5873 16
2012 S Liang, C Zhang, J Sarmiento, DM Standley Protein loop modeling with optimized backbone potential functions JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8, 1820-1827 14
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, 1-15 13
2010 DM Standley, R Yamashita, AR Kinjo, H Toh, H Nakamura SeSAW: balancing sequence and structural information in protein functional mapping BIOINFORMATICS, 2010, 26, 1258-1259 13
2020 Y Lee, H Yamada, A Pradipta, JS Ma, M Okamoto, H Nagaoka, ... Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense LIFE SCIENCE ALLIANCE, 2020, 3 12
2020 AA Koesoema, DM Standley, S Ohshima, M Tamura, T Matsuda Control of enantioselectivity in the enzymatic reduction of halogenated acetophenone analogs by substituent positions and sizes TETRAHEDRON LETTERS, 2020, 61, 151820-151820 11
2019 AA Koesoema, Y Sugiyama, Z Xu, DM Standley, M Senda, T Senda, ... Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2019, 103, 9543-9553 11
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi, Y Fauzyah, ... Various miRNAs compensate the role of miR-122 on HCV replication PLOS PATHOGENS, 2020, 16, 1008308 10
2020 S Teraguchi, DS Saputri, MA Llamas-Covarrubias, A Davila, D Diez, ... Methods for sequence and structural analysis of B and T cell receptor repertoires COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2020, 18, 2000-2011 10
2017 J Hirano, T Okamoto, Y Sugiyama, T Suzuki, S Kusakabe, M Tokunaga, ... Characterization of SPP inhibitors suppressing propagation of HCV and protozoa PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 114 (50), E10782-, 2017, 10791 10
2019 AA Koesoema, Y Sugiyama, KT Sriwong, Z Xu, S Verina, DM Standley, ... Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2019, 103, 9529-9541 9
2011 S Teraguchi, Y Kumagai, A Vandenbon, S Akira, DM Standley Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations PHYSICAL REVIEW E, 2011, 84, 62903-62903 9
2010 S Teraguchi, A Patil, DM Standley Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins BMC BIOINFORMATICS, 2010, 11, 1-11 9
2008 DM Standley, H Toh, H Nakamura Functional annotation by sequence‐weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2008, 72, 1333-1351 9
2019 H Fukuda, S Li, L Sardo, JL Smith, K Yamashita, AD Sarca, K Shirakawa, ... Structural determinants of the APOBEC3G N-terminal domain for HIV-1 RNA association FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2019, 9, 129-129 8
2010 RJ Milewski, Y Kumagai, K Fujita, DM Standley, NI Smith Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis IMMUNOME RESEARCH, 2010, 6, 1-10 8
2006 DM Standley, Y Yonezawa, Y Goto, H Nakamura Flexible docking of an amyloid-forming peptide from β2-microglobulin FEBS LETTERS, 2006, 580, 6199-6205 8
2020 Y Liu, WT Soh, A Tada, A Arakawa, S Matsuoka, EE Nakayama, S Li, ... An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies BIORXIV, 2020 7
2019 S Li, J Wilamowski, S Teraguchi, FJ Eerden, J Rozewicki, A Davila, Z Xu, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 7
2012 A Patil, S Teraguchi, H Dinh, K Nakai, DM Standley Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator BIOCOMPUTING, 2012, 2012, 164-175 7
2011 S Liang, C Zhang, DM Standley Protein loop selection using orientation‐dependent force fields derived by parameter optimization PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2011, 79, 2260-2267 7
2002 VA Eyrich, DM Standley, RA Friesner Ab initio protein structure prediction using a size-dependent tertiary folding potential ADVANCES IN CHEMICAL PHYSICS, 2002, 120, 223-264 7
2019 Z Xu, S Li, J Rozewicki, K Yamashita, S Teraguchi, T Inoue, R Shinnakasu, ... Functional clustering of B cell receptors using sequence and structural features MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 769-778 6
2017 B Nosirov, J Billaud, A Vandenbon, D Diez, E Wijaya, KJ Ishii, ... Mapping circulating serum miRNAs to their immune-related target mRNAs ADVANCES AND APPLICATIONS IN BIOINFORMATICS AND CHEMISTRY: AABC, 2017, 10, 1-1 6
2021 J Hirano, S Yoshio, Y Sakai, L Songling, T Suzuki, Y Itoh, H Zhang, ... Hepatitis C virus modulates signal peptide peptidase to alter host protein processing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2021, 118, 2026184118 5
2015 D Hall, S Li, K Yamashita, R Azuma, JA Carver, DM Standley RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure ANALYTICAL BIOCHEMISTRY, 2015, 472, 52-61 5
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 BIOCHEMISTRY, 2012, 2, 1-8 5
2021 N Ikemura, S Taminishi, T Inaba, T Arimori, D Motooka, K Katoh, Y Kirita, ... Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant BIORXIV, 2021 4
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, 61, 151682-151682 3
2014 D Hall, S Li, K Yamashita, R Azuma, JA Carver, DM Standley A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein BIOPHYSICAL CHEMISTRY, 2014, 190, 50-55 3
2013 A Vandenbon, Y Kumagai, S Teraguchi, KM Amada, S Akira, DM Standley A Parzen window-based approach for the detection of locally enriched transcription factor binding sites BMC BIOINFORMATICS, 2013, 14, 1-13 3
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 503 (1-3), 2011, 139-144 3
2021 K Katoh, DM Standley Emerging SARS-CoV-2 variants follow a historical pattern recorded in outgroups infecting non-human hosts COMMUNICATIONS BIOLOGY, 2021, 4, 1-6 2
2014 A Vandenbon, S Teraguchi, O Takeuchi, Y Suzuki, DM Standley Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation BMC GENOMICS, 2014, 15, 1-14 2
2011 AR Kinjo, Y Kumagai, H Dinh, O Takeuchi, DM Standley Functional characterization of protein domains common to animal viruses and mouse BMC GENOMICS, 2011, 12, 1-10 2
2022 S Beppu, M Kinoshita, J Wilamowski, T Suenaga, Y Yasumizu, K Ogawa, ... 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, 12, 1-12 1
2022 A Davila, Z Xu, S Li, J Rozewicki, J Wilamowski, S Kotelnikov, D Kozakov, ... AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence BIOINFORMATICS ADVANCES 2 (1), VBAC, 2022, 15 1
2013 E Kanamori, Y Murakami, J Sarmiento, S LIANG, DM Standley, M Shirota, ... Prediction of protein-protein complex structures BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE …, 2013 1
2008 DM Standley, AR Kinjo, M Lis, M van der Giezen, H Nakamura Structure-based functional annotation of protein sequences guided by comparative models THE SECOND INTERNATIONAL SYMPOSIUM ON OPTIMIZATION AND SYSTEMS BIOLOGY …, 2008 1
2022 N Ikemura, S Taminishi, T Inaba, T Arimori, D Motooka, K Katoh, Y Kirita, ... An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo SCIENCE TRANSLATIONAL MEDICINE, EABN, 2022, 7737 0
2022 YK Chong, S Tartey, Y Yoshikawa, K Imami, S Li, M Yoshinaga, ... Cyclin J–CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism SCIENCE SIGNALING 15 (729), EABM, 2022, 5011 0
2022 M Loza, S Teraguchi, DM Standley, D Diez Unbiased integration of single cell transcriptome replicates NAR GENOMICS AND BIOINFORMATICS 4 (1), LQAC, 2022, 22 0
2022 D Standley An adaptive approach to predicting antibody-antigen complex structures from sequence BIOPHYSICAL JOURNAL 121 (3), 39A, 2022 0
2022 Z Xu, A Davila, J Wiamowski, S Teraguchi, DM Standley Improved antibody-specific epitope prediction using AlphaFold and AbAdapt BIORXIV, 2022 0
2022 Y Saijo-Hamano, AA Sherif, A Pradipta, M Sasai, N Sakai, Y Sakihama, ... Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6 LIFE SCIENCE ALLIANCE, 2022, 5 0
2021 H Arase, Y Liu, N Arase, J Kishikawa, M Hirose, S Li, A Tada, S Matsuoka, ... 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
2021 J Rozewicki, S Li, K Katoh, DM Standley Analysis of Protein Intermolecular Interactions with MAFFT-DASH MULTIPLE SEQUENCE ALIGNMENT, 2021, 163-177 0
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi, Y Fauzyah, ... Various miRNAs are involved in efficient HCV replication BIORXIV, 2020 0
2019 DM Standley, JDO Nieri, S Li, D Schritt, K Yamashita Immunological entity clustering software US PATENT APP. 16/333,875, 2019 0
2017 D Schritt, K Katoh, S Li, DM Standley Modeling Biocatalysts FUTURE DIRECTIONS IN BIOCATALYSIS, 2017, 385-398 0
2016 K Takeda, S Sakakibara, D Motooka, S Nakamura, K Yamashita, ... Identification of nasal resident bacteria as causative allergens in eosinophilic chronic rhinosinusitis EUROPEAN JOURNAL OF IMMUNOLOGY, 2016, 46, 1114-1114 0
2016 S Sakakibara, T Arimori, K Yamashita, H Jinzai, D Motooka, S Nakamura, ... Antigen-specific maturation of autoantibodies in systemic lupus erythematosus EUROPEAN JOURNAL OF IMMUNOLOGY, 2016, 46, 313-314 0
2016 SK Suzuki, J Hirano, T Fukuhara, A Yamashita, K Saito, D Okuzaki, ... Hepatocyte factor JMJD5 regulates HBV replication through interaction with HBx , 2016 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 回日本生物物理学会年会 (2014 年度)) 生物物理 54 (1), S, 2014, 133 0
2012 E Kanamori, Y Tsuchiya, Y Murakami, J Sarmiento, S Liang, D Standley, ... Prediction of Protein-Protein Complex Structures Using a Docking Server, surFit PROTEIN SCIENCE, 2012, 21, 178-178 0
2011 Y YONEZAWA, DM STANDLEY, H SHIMOYAMA, H NAKAMURA A QM/MM Molecular Dynamics Simulation Study of the Cis-Trans Isomerization Process of N-Methylacetamide PEPTIDE SCIENCE: PROCEEDINGS OF THE... JAPANESE PEPTIDE SYMPOSIUM, 2011, 2010, 151-151 0
2010 K Oshima, D Standley, E Kanamori, Y Murakami, T Oroguchi, M Ikeguchi, ... 3P294 Structural modeling for protein complexes using small angle x-ray scattering (Bioinformatics: Structural genomics, The 48th Annual Meeting of the Biophysical Society of … SEIBUTSU BUTSURI 50 (SUPPLEMENT2), S, 2010, 197 0
2010 K Oshima, D Standley, E Kanamori, Y Murakami, T Oroguchi, M Ikeguchi, ... 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 50 (2), S, 2010, 197 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
2008 DM Standley, H Nakamura From structures to functions: annotation by structural bioinformatics TANPAKUSHITSU KAKUSAN KOSO. PROTEIN, NUCLEIC ACID, ENZYME, 2008, 53, 638-644 0
2008 Y Tsuchiya, E Kanamori, DM Standley, H Nakamura, K Kinoshita Development of a scoring method for predicting protein complex structures ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 64, C227-C, 2008, 227 0
2008 DM Standley, AR Kinjo, H Nakamura Functional annotation by sequence-weighted structural alignments ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 64, C460-C, 2008, 460 0
2007 DM Standley, H Toh, H Nakamura S08I2 Functional Annotation Sequence-weighted Structure Alignments (Bioinformatics in the Era of Structural Proteomics) SEIBUTSU BUTSURI 47 (SUPPLEMENT), S, 2007, 11 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 of EABS & BSJ … SEIBUTSU BUTSURI 46 (SUPPLEMENT2), S, 2006, 267 0
2005 H Nakamura, N Ito, R Yamashita, D Standley, A Paehler, A Yoshihara PDBML: the XML-based Database and its Applications ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 61, C128-C, 2005, 128 0
2005 DM Standley, H Nakamura Beyond Text-based Queries at the Protein Data Bank, Japan ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 61, C482-C, 2005, 482 0
2002 DM STANDLEY AB 1N1T1O PROTE1N STRUCTURE PRED1CT1ON US1NG A S1ZE-DEPENDENT TERT1ARY FOLD1NG POTENT1AL COMPUTATIONAL METHODS FOR PROTEIN FOLDING, 2002, 223 0
2001 YL An, D Standley, D Pincus, V Eyrich, RA Friesner Fold recognition using composite structural templates followed by constrained global minimization. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 222, U411-U, 2001, 411 0
2001 DM Standley, VA Eyrich, Y An, DL Pincus, JR Gunn, RA Friesner Ab Initio: Prediction Reports-Protein Structure Prediction Using a Combination of Sequence-Based Alignment, Constrained Energy Minimization, and Structural Alignment Published … PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2001, 133-139 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 CHEMISTRY AND MOLECULAR BIOLOGY, 2000, 57-71 0
1998 DM Standley Protein tertiary structure prediction by constrained and unconstrained energy minimization COLUMBIA UNIVERSITY, 1998 0
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