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1

Protein tertiary structure prediction using a branch and bound algorithm

Volker A. Eyrich, Daron M. Standley, Anthony K. Felts, Richard A. Friesner

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

1999

Langue:

english

Fichier:

PDF, 217 KB

english, 1999

2

Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation

Uehata, Takuya, Iwasaki, Hidenori, Vandenbon, Alexis, Matsushita, Kazufumi, Hernandez-Cuellar, Eduardo, Kuniyoshi, Kanako, Satoh, Takashi, Mino, Takashi, Suzuki, Yutaka, Standley, Daron M., Tsujimura,

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.74 MB

english, 2013

3

Tertiary structure prediction of mixed α/β proteins via energy minimization

Daron M. Standley, John R. Gunn, Richard A. Friesner, Ann E. McDermott

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

1998

Langue:

english

Fichier:

PDF, 257 KB

english, 1998

4

Binding Energetics of Ferredoxin-NADP+ Reductase with Ferredoxin and Its Relation to Function

Prof. Young-Ho Lee, Prof. Takahisa Ikegami, Dr. Daron M. Standley, Prof. Kazumasa Sakurai, Prof. Toshiharu Hase, Prof. Yuji Goto

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2011

5

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

Shide Liang, Yaoqi Zhou, Nick Grishin, Daron M. Standley

Journal:

Journal of Computational Chemistry

Année:

2011

Langue:

english

Fichier:

PDF, 210 KB

english, 2011

6

Prediction of dinucleotide-specific RNA-binding sites in proteins

Michael Fernandez, Yutaro Kumagai, Daron M Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad

Journal:

BMC Bioinformatics

Année:

2011

Langue:

english

Fichier:

PDF, 836 KB

english, 2011

7

Functional characterization of protein domains common to animal viruses and mouse

Akira R Kinjo, Yutaro Kumagai, Huy Dinh, Osamu Takeuchi, Daron M Standley

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 778 KB

english, 2011

8

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster

Jinzen Ikebe, Daron M. Standley, Haruki Nakamura, Junichi Higo

Journal:

Protein Science

Année:

2011

Langue:

english

Fichier:

PDF, 602 KB

english, 2011

9

Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment

Daron M. Standley, Volker A. Eyrich, Yuling An, David L. Pincus, John R. Gunn, Richard A. Friesner

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2001

Langue:

english

Fichier:

PDF, 794 KB

english, 2001

10

Detecting local structural similarity in proteins by maximizing number of equivalent residues

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 221 KB

english, 2004

11

Docking of protein molecular surfaces with evolutionary trace analysis

Eiji Kanamori, Yoichi Murakami, Yuko Tsuchiya, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 311 KB

english, 2007

12

Functional annotation by sequence-weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2008

Langue:

english

Fichier:

PDF, 649 KB

english, 2008

13

Protein loop selection using orientation-dependent force fields derived by parameter optimization

Shide Liang, Chi Zhang, Daron M. Standley

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2011

Langue:

english

Fichier:

PDF, 296 KB

english, 2011

14

Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide

Yasushige Yonezawa, Daron M. Standley, Haruki Nakamura

Journal:

Chemical Physics Letters

Année:

2011

Langue:

english

Fichier:

PDF, 290 KB

english, 2011

15

Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase

Karleigh Hamblin, Daron M. Standley, Matthew B. Rogers, Alexandra Stechmann, Andrew J. Roger, Robin Maytum, Mark Van Der Giezen

Journal:

Molecular Microbiology

Année:

2008

Langue:

english

Fichier:

PDF, 687 KB

english, 2008

16

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

Matsushita, Kazufumi, Takeuchi, Osamu, Standley, Daron M., Kumagai, Yutaro, Kawagoe, Tatsukata, Miyake, Tohru, Satoh, Takashi, Kato, Hiroki, Tsujimura, Tohru, Nakamura, Haruki

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 910 KB

english, 2009

17

Systems biology approaches to toll-like receptor signaling

Alexis Vandenbon, Shunsuke Teraguchi, Shizuo Akira, Kiyoshi Takeda, Daron M. Standley

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Année:

2012

Langue:

english

Fichier:

PDF, 844 KB

english, 2012

18

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias, Chi Zhang

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 674 KB

english, 2010

19

Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins

Shunsuke Teraguchi, Ashwini Patil, Daron M Standley

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 809 KB

english, 2010

20

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures

Daron M Standley, Hiroyuki Toh, Haruki Nakamura

Journal:

BMC Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 607 KB

english, 2005

21

ASH structure alignment package: Sensitivity and selectivity in domain classification

Daron M Standley, Hiroyuki Toh, Haruki Nakamura

Journal:

BMC Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 401 KB

english, 2007

22

A branch and bound algorithm for protein structure refinement from sparse NMR data sets

Daron M. Standley, Volker A. Eyrich, Anthony K. Felts, Richard A. Friesner, Ann E. McDermott

Journal:

Journal of Molecular Biology

Année:

1999

Langue:

english

Fichier:

PDF, 1.41 MB

english, 1999

23

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set

Volker A Eyrich, Daron M Standley, Richard A Friesner

Journal:

Journal of Molecular Biology

Année:

1999

Langue:

english

Fichier:

PDF, 536 KB

english, 1999

24

The Transcription Factor Jdp2 Controls Bone Homeostasis and Antibacterial Immunity by Regulating Osteoclast and Neutrophil Differentiation

Maruyama, Kenta, Fukasaka, Masahiro, Vandenbon, Alexis, Saitoh, Tatsuya, Kawasaki, Takumi, Kondo, Takeshi, Yokoyama, Kazunari K., Kidoya, Hiroyasu, Takakura, Nobuyuki, Standley, Daron, Takeuchi, Osamu

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 1.72 MB

english, 2012

25

Flexible docking of an amyloid-forming peptide from β2-microglobulin

Daron M. Standley, Yasushige Yonezawa, Yuji Goto, Haruki Nakamura

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 717 KB

english, 2006

26

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis

Robert J Milewski, Yutaro Kumagai, Katsumasa Fujita, Daron M Standley, Nicholas I Smith

Journal:

Immunome Research

Année:

2010

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2010

27

The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1

Iwasaki, Hidenori, Takeuchi, Osamu, Teraguchi, Shunsuke, Matsushita, Kazufumi, Uehata, Takuya, Kuniyoshi, Kanako, Satoh, Takashi, Saitoh, Tatsuya, Matsushita, Mutsuyoshi, Standley, Daron M, Akira, Shi

Journal:

Nature Immunology

Année:

2011

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2011

28

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations

Teraguchi, Shunsuke, Kumagai, Yutaro, Vandenbon, Alexis, Akira, Shizuo, Standley, Daron M

Journal:

Physical Review E

Année:

2011

Langue:

english

Fichier:

PDF, 318 KB

english, 2011

29

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription

Alexis Vandenbon, Yutaro Kumagai, Shizuo Akira, Daron M Standley

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 993 KB

english, 2012

30

A novel function prediction approach using protein overlap networks

Shide Liang, Dandan Zheng, Daron M Standley, Huarong Guo, Chi Zhang

Journal:

BMC Systems Biology

Année:

2013

Langue:

english

Fichier:

PDF, 310 KB

english, 2013

31

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein

Hall, Damien, Li, Songling, Yamashita, Kazuo, Azuma, Ryuzo, Carver, John A., Standley, Daron M.

Journal:

Biophysical Chemistry

Année:

2014

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2014

32

The Second Messenger Phosphatidylinositol-5-Phosphate Facilitates Antiviral Innate Immune Signaling

Kawasaki, Takumi, Takemura, Naoki, Standley, Daron M., Akira, Shizuo, Kawai, Taro

Journal:

Cell Host & Microbe

Année:

2013

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2013

33

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

Shirai, Hiroki, Ikeda, Kazuyoshi, Yamashita, Kazuo, Tsuchiya, Yuko, Sarmiento, Jamica, Liang, Shide, Morokata, Tatsuaki, Mizuguchi, Kenji, Higo, Junichi, Standley, Daron M., Nakamura, Haruki

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 477 KB

english, 2014

34

Membrane Attachment Facilitates Ligand Access to the Active Site in Monoamine Oxidase A

Apostolov, Rossen, Yonezawa, Yasushige, Standley, Daron M., Kikugawa, Gota, Takano, Yu, Nakamura, Haruki

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 6.81 MB

english, 2009

35

Protein Loop Modeling with Optimized Backbone Potential Functions

Liang, Shide, Zhang, Chi, Sarmiento, Jamica, Standley, Daron M.

Journal:

Journal of Chemical Theory and Computation

Année:

2012

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2012

36

Higher Order Structure Contributes to Specific Differences in Redox Potential and Electron Transfer Efficiency of Root and Leaf Ferredoxins †

Gou, Ping, Hanke, Guy T., Kimata-Ariga, Yoko, Standley, Daron M., Kubo, Atsushi, Taniguchi, Isao, Nakamura, Haruki, Hase, Toshiharu

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 353 KB

english, 2006

37

Deconstructing RNA: optical measurement of composition and structure

Hobro, Alison J., Standley, Daron M., Ahmad, Shandar, Smith, Nicholas I.

Journal:

Physical Chemistry Chemical Physics

Année:

2013

Langue:

english

Fichier:

PDF, 1.86 MB

english, 2013

38

RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

Hall, Damien, Li, Songling, Yamashita, Kazuo, Azuma, Ryuzo, Carver, John A., Standley, Daron M.

Journal:

Analytical Biochemistry

Année:

2015

Langue:

english

Fichier:

PDF, 3.81 MB

english, 2015

39

RabGDIα is a negative regulator of interferon-γ–inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii

Ohshima, Jun, Sasai, Miwa, Liu, Jianfa, Yamashita, Kazuo, Ma, Ji Su, Lee, Youngae, Bando, Hironori, Howard, Jonathan C., Ebisu, Shigeyuki, Hayashi, Mikako, Takeda, Kiyoshi, Standley, Daron M., Frickel

Journal:

Proceedings of the National Academy of Sciences

Année:

2015

Langue:

english

Fichier:

PDF, 1.76 MB

english, 2015

40

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

Katoh, Kazutaka, Standley, Daron M.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 752 KB

english, 2016

41

Arid5a regulates naive CD4 + T cell fate through selective stabilization of Stat3 mRNA

Masuda, Kazuya, Ripley, Barry, Nyati, Kishan Kumar, Dubey, Praveen Kumar, Zaman, Mohammad Mahabub-Uz, Hanieh, Hamza, Higa, Mitsuru, Yamashita, Kazuo, Standley, Daron M., Mashima, Tsukasa, Katahira, Ma

Journal:

Journal of Experimental Medicine

Année:

2016

Langue:

english

Fichier:

PDF, 2.75 MB

english, 2016

42

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation

Vandenbon, Alexis, Teraguchi, Shunsuke, Takeuchi, Osamu, Suzuki, Yutaka, Standley, Daron M

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2014

43

Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines

Hayashi, Masayuki, Aoshi, Taiki, Haseda, Yasunari, Kobiyama, Kouji, Wijaya, Edward, Nakatsu, Noriyuki, Igarashi, Yoshinobu, Standley, Daron M., Yamada, Hiroshi, Honda-Okubo, Yoshikazu, Hara, Hiromitsu

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2017

44

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions

Yokogawa, Mariko, Tsushima, Takashi, Noda, Nobuo N., Kumeta, Hiroyuki, Enokizono, Yoshiaki, Yamashita, Kazuo, Standley, Daron M., Takeuchi, Osamu, Akira, Shizuo, Inagaki, Fuyuhiko

Journal:

Scientific Reports

Année:

2016

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2016

45

Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense

Sasai, Miwa, Sakaguchi, Naoya, Ma, Ji Su, Nakamura, Shuhei, Kawabata, Tsuyoshi, Bando, Hironori, Lee, Youngae, Saitoh, Tatsuya, Akira, Shizuo, Iwasaki, Akiko, Standley, Daron M, Yoshimori, Tamotsu, Ya

Journal:

Nature Immunology

Année:

2017

Langue:

english

Fichier:

PDF, 6.28 MB

english, 2017

46

Structural basis for the assembly of the Ragulator-Rag GTPase complex

Yonehara, Ryo, Nada, Shigeyuki, Nakai, Tomokazu, Nakai, Masahiro, Kitamura, Ayaka, Ogawa, Akira, Nakatsumi, Hirokazu, Nakayama, Keiichi I., Li, Songling, Standley, Daron M., Yamashita, Eiki, Nakagawa,

Journal:

Nature Communications

Année:

2017

Langue:

english

Fichier:

PDF, 6.37 MB

english, 2017

47

Arid5a stabilizes OX40 mRNA in murine CD4 + T cells by recognizing a stem-loop structure in its 3'UTR

Hanieh, Hamza, Masuda, Kazuya, Metwally, Hozaifa, Chalise, Jaya P., Mohamed, Maged, Nyati, Kishan K., Standley, Daron M., Li, Songling, Higa, Mitsuru, Zaman, Mohammad M., Kishimoto, Tadamitsu

Journal:

European Journal of Immunology

Année:

2017

Langue:

english

Fichier:

PDF, 2.42 MB

english, 2017

48

TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a

Nyati, Kishan K., Masuda, Kazuya, Zaman, Mohammad Mahabub-Uz, Dubey, Praveen K., Millrine, David, Chalise, Jaya P., Higa, Mitsuru, Li, Songling, Standley, Daron M., Saito, Kazunobu, Hanieh, Hamza, Kis

Journal:

Nucleic Acids Research

Année:

2017

Langue:

english

Fichier:

PDF, 8.47 MB

english, 2017

49

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 2006)

Standley, Daron M., Toh, Hiroyuki, Nakamura, Haruki

Journal:

Seibutsu Butsuri

Année:

2006

Langue:

english

Fichier:

PDF, 153 KB

english, 2006

50

S08I2 Functional Annotation Sequence-weighted Structure Alignments(Bioinformatics in the Era of Structural Proteomics)

Standley, Daron M., Toh, Hiroyuki, Nakamura, Haruki

Journal:

Seibutsu Butsuri

Année:

2007

Langue:

english

Fichier:

PDF, 201 KB

english, 2007