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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
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, 30, 772-780 | 15216 |
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 | 862 |
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 | 458 |
2014 | K Katoh, DM Standley | MAFFT: iterative refinement and additional methods | MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 | 265 |
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 | 227 |
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 | 222 |
2016 | K Katoh, DM Standley | A simple method to control over-alignment in the MAFFT multiple sequence alignment program | BIOINFORMATICS, 2016, 32, 1933-1942 | 213 |
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 | 212 |
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 | 195 |
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 | 188 |
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 | 133 |
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 | 123 |
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 | 122 |
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 | 117 |
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 | 98 |
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 | 95 |
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 | 92 |
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 | 74 |
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 | 72 |
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 | 59 |
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 | 58 |
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 | 52 |
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 | 52 |
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 | 50 |
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 | 49 |
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, 8-8 | 49 |
2007 | DM Standley, H Toh, H Nakamura | ASH structure alignment package: sensitivity and selectivity in domain classification | BMC BIOINFORMATICS, 2007, 8, 116-116 | 47 |
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 | 44 |
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 | 44 |
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 | 44 |
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 | 43 |
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 | 42 |
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 | 42 |
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 | 39 |
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 | 38 |
2011 | S Liang, D Zheng, C Zhang, DM Standley | Fast and accurate prediction of protein side-chain conformations | BIOINFORMATICS, 2011, 27, 2913-2914 | 38 |
2010 | K Zhuo, R Cui, WM Ye, M Luo, H Wang, X Hu, J Liao | Morphological and molecular characterization of Aphelenchoides fujianensis n. sp.(Nematoda: Aphelenchoididae) from Pinus massoniana in China | ZOOTAXA, 2010, 2509, 39-52 | 36 |
2011 | M Fernandez, Y Kumagai, DM Standley, A Sarai, K Mizuguchi, S Ahmad | Prediction of dinucleotide-specific RNA-binding sites in proteins | BMC BIOINFORMATICS 12 (S13), S, 2011, 5 | 35 |
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 | 35 |
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, 899-899 | 34 |
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 | 34 |
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, 221-221 | 32 |
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 | 30 |
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 | 30 |
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 | 30 |
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 | 29 |
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 | 28 |
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 | 27 |
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 | 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 | 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 | 24 |
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 | 24 |
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 | 21 |
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 | 21 |
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 | 21 |
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 | 19 |
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 | 17 |
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 | 17 |
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, 61-61 | 17 |
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 | 17 |
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 | 17 |
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 | 16 |
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 | 15 |
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 | 14 |
2014 | T Hirano, Y Iesato, Y Toriyama, A Imai, T Murata | Detection of fovea-threatening diabetic macular edema by optical coherence tomography to maintain good vision by prophylactic treatment | OPHTHALMIC RESEARCH, 2014, 52, 65-73 | 14 |
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 | 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 | 12 |
2007 | J Liao, K Zhuo, S Yu, X Li, D Li | Bursaphelenchus uncispicularis n. sp.(Nematoda: Parasitaphelenchidae) from Pinus yunnanensis in China | NEMATOLOGY, 2007, 9, 237-242 | 12 |
2012 | A Vandenbon, Y Kumagai, S Akira, DM Standley | A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription | BMC GENOMICS 13 (S7), S, 2012, 11 | 11 |
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 | 11 |
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 | 10 |
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 | 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 11 (S7), S, 2010, 7 | 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 |
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 |
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 |
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 | 7 |
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 103 (23-24), 2019, 9543-9553 | 6 |
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 | 6 |
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 | 6 |
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 | 5 |
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 | 5 |
2012 | DM Standley, M van der Giezen | Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly | RES. REP. BIOCHEM, 2012, 2, 1-8 | 5 |
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 103 (23-24), 2019, 9529-9541 | 4 |
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 | 4 |
2020 | AA Koesoema, DM Standley, T Senda, T Matsuda | Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications | APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2020, 1-13 | 3 |
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 | 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, 26-26 | 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 |
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, 2020, 13 | 2 |
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 | 2 |
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, 151820 | 2 |
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, 151682 | 2 |
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 | 2 |
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 | 2 |
2019 | S Li, J Wilamowski, S Teraguchi, FJ van Eerden, J Rozewicki, A Davila, ... | Structural modeling of lymphocyte receptors and their antigens | IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 | 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 15 (S10), S, 2014, 4 | 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 |
2013 | E KANAMORI, Y MURAKAMI, JOY SARMIENTO, S LIANG, ... | 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 |
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 | 0 |
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 | 0 |
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 | 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 | AA Koesoema, Y Sugiyama, Z Xu, DM Standley, M Senda, T Senda, ... | Correction to: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain. | APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 103 (23-24), 2019, 9555 | 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 |
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 |
2013 | Y Furukawa, S Teraguchi, T Ikegami, Y Suenari, O Dagliyan, L Jin, D Hall, ... | Calcium-dependent Unfolding of the STIM1 EF-SAM Domain Drives Cooperative Calcium Influx: 362 | PROTEIN SCIENCE, 2013, 22, 141-142 | 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: 317 | PROTEIN SCIENCE, 2012, 21 | 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 | D Kuroda, H Shirai, M Lis, A Kinjo, D Standley, H Nakamura | Structural classification and modeling of antibody hypervariable loops: knowledge-based approaches: 242 | PROTEIN SCIENCE, 2009, 18 | 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, 638-638 | 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 |
2006 | DM Standley, R Yamashita, K Ichikawa, K Kinoshita, N Ito, H Nakamura | New Web Services for Structural Genomics at PDBj: Development of POBML and its Applications | ABSTRACT BOOK OF THE 4TH ISGO INTERNATIONAL CONFERENCE ON STRUCTURAL GENOMICS, 2006 | 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 |
1999 | DM Standley | Protein tertiary structure prediction by constrained and unconstrained energy minimization. | , 1999 | 0 |
1939 | DC Koester, SI Awan, DB Werz, YH Lee, T Ikegami, DM Standley, ... | Don’t risk missing out! Subscribe to ChemBioChem. Contact www. wileycustomerhelp. com | CHEMBIOCHEM, 1939, 2011, 2011-2011 | 0 |