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Submissions from 2012

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Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction, Saras Saraswathi, Juan Luis Fernandez-Martinez, Andrzej Kolinski, Robert L. Jernigan, and Andrzej Kloczkowski

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The Importance of Slow Motions for Protein Functional Loops, Aris Skliros, Michael T. Zimmermann, Debkanta Chakraborty, Saras Saraswathi, Ataur R. Katebi, Sumudu P. Leelananda, Andrzej Kloczkowski, and Robert L. Jernigan

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Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions, Matthew Edward Studham and Gustavo C. Macintosh

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Self-Assembly and Biphasic Iron-Binding Characteristics of Mms6, A Bacterial Protein That Promotes the Formation of Superparamagnetic Magnetite Nanoparticles of Uniform Size and Shape, Lijun Wang, Tanya Prozorov, Pierre E. Palo, Xunpei Liu, David Vaknin, Ruslan Prozorov, Surya K. Mallapragada, and Marit Nilsen-Hamilton

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Characterization of CYP76M5–8 Indicates Metabolic Plasticity within a Plant Biosynthetic Gene Cluster, Qiang Wang, Matthew L. Hillwig, Kazunori Okada, Kohei Yamazaki, Yisheng Wu, Sivakumar Swaminathan, Hisakazu Yamane, and Reuben J. Peters

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Interfacial Properties and Iron Binding to Bacterial Proteins That Promote the Growth of Magnetite Nanocrystals: X-ray Reflectivity and Surface Spectroscopy Studies, Wenjie Wang, Wei Bu, Lijun Wang, Pierre E. Palo, Surya K. Mallapragada, Marit Nilsen-Hamilton, and David Vaknin

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Medicinal Plants: A Public Resource for Metabolomics and Hypothesis Development, Eve Syrkin Wurtele, Joe Chappell, A. Daniel Jones, Mary Dawn Celiz, Nick Ransom, Manhoi Hur, Ludmila Rizshsky, Matthew Crispin, Philip Dixon, Jia Liu, Mark P. Widrlechner, and Basil J. Nikolau

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Functional characterization of wheat copalyl diphosphate synthases sheds light on the early evolution of labdane-related diterpenoid metabolism in the cereals, Yisheng Wu, Ke Zhou, Tomonobu Toyomasu, Chizu Sugawara, Madoka Oku, Shiho Abe, Masami Usui, Wataru Mitsuhashi, Makiko Chono, Peter M. Chandler, and Reuben J. Peters

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Genetic evidence for natural product-mediated plant–plant allelopathy in rice (Oryza sativa), Meimei Xu, Rita Galhano, Philipp Wiemann, Emilio Bueno, Mollie Tiernan, William Wu, Ill-Min Chung, Jonathan Gershenzon, Bettina Tudzynski, Ane Sesma, and Reuben J. Peters

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An RNA Aptamer-Based Microcantilever Sensor To Detect the Inflammatory Marker, Mouse Lipocalin-2, Lijie Zhai, Tianjiao Wang, Kyungho Kang, Yue Zhao, Pranav Shrotriya, and Marit Nilsen-Hamilton

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Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis, Ke Zhou, Yang Gao, Julie A. Hoy, Francis M. Mann, Richard B. Honzatko, and Reuben J. Peters

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Functional characterization of wheat ent-kaurene(-like) synthases indicates continuing evolution of labdane-related diterpenoid metabolism in the cereals, Ke Zhou, Meimei Xu, Mollie Tiernan, Qian Xie, Tomonobu Toyomasu, Chizu Sugawara, Madoka Oku, Masami Usui, Wataru Mitsuhashi, Makiko Chono, and Peter M. Chandler

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Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein, Michael T. Zimmermann and Robert L. Jernigan

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Effect of Isotopically Sensitive Branching on Product Distribution for Pentalenene Synthase: Support for a Mechanism Predicted by Quantum Chemistry, Liansuo Zu, Meimei Xu, Michael W. Lodewyk, David E. Cane, Reuben J. Peters, and Dean J. Tantillo

Submissions from 2011

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A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans, Yihong Chen, Ethel Apolinario, Libuse Brachova, Zvi Kelman, Zhuo Li, Basil Nikolau, Lucas John Showman, Kevin Sowers, and John Orban

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An Interaction between the Walker A and D-loop Motifs Is Critical to ATP Hydrolysis and Cooperativity in Bacteriophage T4 Rad50, Metzere Bierlein De la Rosa and Scott W. Nelson

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MultiBody Coarse-Grained Potentials for Native Structure Recognition and Quality Assessment of Protein Models, Pawel Gniewek, Sumudu P. Leelananda, Andrzej Kolinski, Robert L. Jernigan, and Andrzej Kloczkowski

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Biochemical Characterization of Bacteriophage T4 Mre11-Rad50 Complex, Timothy J. Herdendorf; Dustin William Albrecht; Stephen J. Benkovic; and Scott W, Nelson

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Functional Evaluation of Bacteriophage T4 Rad50 Signature Motif Residues, Timothy J. Herdendorf and Scott W. Nelson

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Diterpenoid biopolymers: New directions for renewable materials engineering, Matthew L. Hillwig, Francis M. Mann, and Reuben J. Peters

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Domain loss has independently occurred multiple times in plant terpene synthase evolution, Matthew L. Hillwig, Meimei Xu, Tomonobu Toyomasu, Mollie S. Tiernan, Gao Wei, Guanghong Cui, Luqi Huang, and Reuben J. Peters

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Statistical Measures on Residue-Level Protein Structural Properties, Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, and Zhijun Wu

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Purification, Crystallization and Preliminary Crystallographic Analysis of the SH2 Domain of IL-2-inducible T-cell Kinase, Raji E. Joseph, Nathaniel D. Ginder, Julie A. Hoy, Jay C. Nix, Richard B. Honzatko, and Amy H. Andreotti

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Aptamer Functionalized Microcantilever Sensors for Cocaine Detection, Kyungho Kang, Ashish Sachan, Marit Nilsen-Hamilton, and Pranav Shrotriya

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Structure and mechanism of the diterpene cyclase ent-copalyl diphosphate synthase, Mustafa Köksal, Huayou Hu, Robert M. Coates, Reuben J. Peters, and David D. Christianson

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Exploration of the relationship between topology and designability of conformations, Sumudu P. Leelananda, Fadi Towfic, Robert L. Jernigan, and Andrzej Kloczkowski

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A Novel Labda-7,13E-dien-15-ol-Producing Bifunctional Diterpene Synthase from Selaginella moellendorffii, Sibongile Mafu, Matthew L. Hillwig, and Reuben J. Peters

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Rv0989c encodes a novel (E)-geranyl diphosphate synthase facilitating decaprenyl diphosphate biosynthesis in Mycobacterium tuberculosis, Francis M. Mann, Jill A. Thomas, and Reuben J. Peters

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Magnesium depletion triggers production of an immune modulating diterpenoid in Mycobacterium tuberculosis, Francis M. Mann, Brian C. VanderVen, and Reuben J. Peters

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Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals, Dana Morrone, Matthew L. Hillwig, Matthew E. Mead, Luke Lowry, D. Bruce Fulton, and Reuben J. Peters

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Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli, Chih-Chia Su, Feng Long, Michael T. Zimmermann, Kanagalaghatta R. Rajashankar, Robert L. Jernigan, and Edward W. Yu

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CYP99A3: functional identification of a diterpene oxidase from the momilactone biosynthetic gene cluster in rice, Qiang Wang, Matthew L. Hillwig, and Reuben J. Peters

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Analysis of protein dynamics using local-DME calculations, Di Wu, Stephen Smith, Hannah Mahan, Robert L. Jernigan, and Zhijun Wu

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Parsing a multifunctional biosynthetic gene cluster from rice: Biochemical characterization of CYP71Z6 & 7, Yinsheng Wu, Matthew L. Hillwig, Qiang Wang, and Reuben J. Peters

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Deficiency of maize starch-branching enzyme i results in altered starch fine structure, decreased digestibility and reduced coleoptile growth during germination, Huan Xia, Marna Yandeau-Nelson, Donald B. Thompson, and Mark J. Guiltinan

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Electrostatic effects on (di)terpene synthase product outcome, Ke Zhou and Reuben J. Peters

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MAVENs: motion analysis and visualization of elastic networks and structural ensembles, Michael T. Zimmermann, Andrzej Kloczkowski, and Robert L. Jernigan

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Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models, Michael T. Zimmermann, Sumudu P. Leelananda, Pawel Gniewek, Yaping Feng, Robert L. Jernigan, and Andrzej Kloczkowski

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Immunoglobulin Structure Exhibits Control over CDR Motion, Michael T. Zimmermann, Aris Skliros, Andrzej Kloczkowski, and Robert L. Jernigan

Submissions from 2010

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T-Cell Signaling Regulated by the Tec Family Kinase, Itk, Amy H. Andreotti, Pamela L. Schwartzberg, Raji E. Joseph, and Leslie J. Berg

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T Cell Specific Adapter Protein (TSAd) Interacts with Tec Kinase ITK to Promote CXCL12 Induced Migration of Human and Murine T Cells, Tone Berge, Vibeke Sundvold-Gjerstad, Stine Granum, Thorny Cecilie Bie Andersen, Gunn B. Holthe, Lena Claesson-Welsh, Amy H. Andreotti, Marit Inngjerdingen, and Anne Spurkland

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Diterpene cyclases and the nature of the isoprene fold, Rong Cao, Yonghui Zhang, Francis M. Mann, Cancan Huang, Dushyant Mukkamala, Michael P. Hudock, Matthew Mead, Sladjana Prisic, Ke Wang, Fu-Yang Lin, Ting-Kai Chang, Reuben Peters, and Eric Oldfield

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Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials, Yaping Feng, Andrzej Kloczkowski, and Robert L. Jernigan

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Petunia nectar proteins have ribonuclease activity, Melissa Sue Hillwig, Xiaoteng Liu, Guangyu Liu, Robert W. Thornburg, and Gustavo C. Macintosh

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Controlling the Activity of the Tec Kinase Itk by Mutation of the Phenylalanine Gatekeeper Residue, Raji E. Joseph and Amy H. Andreotti

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Identification of an Allosteric Signaling Network within Tec Family Kinases, Raji E. Joseph, Qian Xie, and Amy H. Andreotti

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Structural interpretation of protein-protein interaction network, Ataur R. Katebi, Andrzej Kloczkowski, and Robert L. Jernigan

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Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport, Feng Long, Chih-Chia Su, Michael T. Zimmermann, Scott E. Boyken, Kanagalaghatta R. Rajashankar, Robert L. Jernigan, and Edward W. Yu

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A Single Residue Switch for Mg2+-dependent Inhibition Characterizes Plant Class II Diterpene Cyclases from Primary and Secondary Metabolism, Francis M. Mann, Sladjana Prisic, Emily K. Davenport, Mara K. Determan, Robert M. Coates, and Reuben J. Peters

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Synthesis of (±)-Nosyberkol (Isotuberculosinol, Revised Structure of Edaxadiene) and (±)-Tuberculosinol, Nathan Maugel, Francis M. Mann, Matthew L. Hillwig, Reuben J. Peters, and Barry B. Snider

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Increasing diterpene yield with a modular metabolic engineering system in E. coli: comparison of MEV and MEP isoprenoid precursor pathway engineering, Dana Morrone, Luke Lowry, Mara K. Determan, David M. Hershey, Meimei Xu, and Reuben J. Peters

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Two rings in them all: The labdane-related diterpenoids, Reuben J. Peters

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Echinacea-induced cytosolic Ca2+ elevation in HEK293, Lankun Wu, Eric W. Rowe, Ksenija Jeftinija, Srdija Jeftinija, Ludmila Rizhsky, Basil Nikolau, Jodi McKay, Marian L. Kohut, and Eve Wurtele

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Parity is associated with an expanded macrophage population in the mammary gland, Wei Zhao, Clinton J. Grubbs, Ronald K. Myers, and Marit Nilsen-Hamilton

Submissions from 2009

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Refinement of Under-Determined Loops of Human Prion Protein by Database-Derived Distance Constraints, Feng Cui, Kriti Mukhopadhyay, Won-Bin Young, Robert L. Jernigan, and Zhijun Wu

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The energy profiles of atomic conformational transition intermediates of adenylate kinase, Yaping Feng, Lei Yang, Andrzej Kloczkowski, and Robert L. Jernigan

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A Functional Genomics Approach to Tanshinone Biosynthesis Provides Stereochemical Insights, Wei Gao, Matthew L. Hillwig, Luqi Huang, Guanghong Cui, Xueyong Wang, Jianqiang Kong, Bin Yang, and Reuben J. Peters

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Conformational snapshots of Tec kinases during signaling, Raji E. Joseph and Amy H. Andreotti

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SH2-Dependent Autophosphorylation within the Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, and Amy H. Andreotti

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Distance Matrix-Based Approach to Protein Structure Prediction, Andrzej Kloczkowski, Robert Jernigan, Zhijun Wu, Guang Song, Lei Yang, Andrzej Kolinski, and Piotr Pokarowski

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Collective Dynamics of the Ribosomal Tunnel Revealed by Elastic Network Modeling, Ozge Kurkcuoglu, Zeynep Kurkcuoglu, Pemra Doruker, and Robert L. Jernigan

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Characterization and Inhibition of a Class II Diterpene Cyclase from Mycobacterium tuberculosis: Implications for tuberculosis, Francis M. Mann, Sladjana Prisic, Huayou Hu, Meimei Xu, Robert M. Coates, and Reuben J. Peters

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Edaxadiene: A New Bioactive Diterpene from Mycobacterium tuberculosis, Francis M. Mann, Meimei Xu, Xiaoming Chen, D. Bruce Fulton, David G. Russell, and Reuben J. Peters

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α3β1 integrin in epidermis promotes wound angiogenesis and keratinocyte-to-endothelial-cell crosstalk through the induction of MRP3, Kara Mitchell, Charles Szekeres, Vincenzo Milano, Kimberly B. Svenson, Marit Nilsen-Hamilton, Jordan A. Kreidberg, and C. Michael DiPersio

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Book review of "Aptamers in Bioanalysis", Marit Nilsen-Hamilton

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Protein flexibility: coordinate uncertainties and interpretation of structural differences, Alexander A. Rashin, Abraham H. L. Rashin, and Robert L. Jernigan

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Iterative cluster-NMA (icNMA): A tool for generating conformational transitions in proteins, Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan, and Gregory S. Chirikjian

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Proline isomerization preorganizes the Itk SH2 domain for binding the Itk SH3 domain, Andrew J. Severin, Raji E. Joseph, Scott E. Boyken, D. Bruce Fulton, and Amy H. Andreotti

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PRTAD: A Database for Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, and Zhijun Wu

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CYP76M7 Is an ent-Cassadiene C11α-Hydroxylase Defining a Second Multifunctional Diterpenoid Biosynthetic Gene Cluster in Rice, Sivakumar Swaminathan, Dana Morrone, Qiang Wang, D. Bruce Fulton, and Reuben J. Peters

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Computational and Experimental Analyses Converge to Reveal a Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity, Tianjiao Wang, Julie A. Hoy, Monica H. Lamm, and Marit Nilsen-Hamilton

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Comparisons of Experimental and Computed Protein Anisotropic Temperature Factors, Lei Yang, Guang Song, and Robert L. Jernigan

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Investigating the conservation pattern of a putative second terpene synthase divalent metal binding motif in plants, Ke Zhou and Reuben J. Peters

Submissions from 2008

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Substrate Specificity of the 3-Methylcrotonyl Coenzyme A (CoA) and Geranyl-CoA Carboxylases from Pseudomonas aeruginosa, J. A. Aguilar, C. Diaz-Perez, A. L. Diaz-Perez, J. S. Rodriguez-Zavala, Basil Nikolau, and J. Campos-Garcia

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Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement, Feng Cui, Robert Jernigan, and Zhijun Wu

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Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron, Yaping Feng, Robert L. Jernigan, and Andrzej Kloczkowski

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Bacterial expression and purification of Interleukin-2 Tyrosine kinase: Single step separation of the chaperonin impurity, Raji E. Joseph and Amy H. Andreotti

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Differential surface stress sensor for detection of chemical and biological species, K. Kang, Marit Nilsen-Hamilton, and Pranav Shrotriya

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Fluorinated Analogs of Malachite Green: Synthesis and Toxicity, George A. Kraus, Insik Jeon, Marit Nilsen-Hamilton, Ahmed M. Awad, Jayeeta Banerjee, and Bahram Parvin

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The ribosome structure controls and directs mRNA entry, translocation and exit dynamics, Ozge Kurkcuoglu, Pemra Doruker, Taner Z. Sen, Andrzej Kloczkowski, and Robert L. Jernigan

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Articulation of three core metabolic processes in Arabidopsis: Fatty acid biosynthesis, leucine catabolism and starch metabolism, Wieslawa I. Mentzen, Jianling Peng, Nick Ransom, Basil Nikolau, and Eve Wurtele

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Increasing Complexity of a Diterpene Synthase Reaction with a Single Residue Switch, Dana Morrone, Meimei Xu, D. Bruce Fulton, Mara K. Determan, and Reuben J. Peters

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Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable, Myron Peto, Andrzej Kloczkowski, Vasant Honavar, and Robert L. Jernigan

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Murine Itk SH3 domain, Andrew Severin, D. Bruce Fulton, and Amy H. Andreotti

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Predicting the order in which contacts are broken during single molecule protein stretching experiments, Joanna I. Sulkowska, Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak, and Robert L. Jernigan

Submissions from 2007

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A Modular Approach for Facile Biosynthesis of Labdane-Related Diterpenes, Anthony Cyr, P. Ross Wilderman, Mara K. Determan, and Reuben J. Peters

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Mechanism and Functional Significance of Itk Autophosphorylation, Raji E. Joseph, D. Bruce Fulton, and Amy H. Andreotti

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The Linker between SH2 and Kinase Domains Positively Regulates Catalysis of the Tec Family Kinases, Raji E. Joseph, Lie Min, and Amy H. Andreotti

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A Remote Substrate Docking Mechanism for the Tec Family Tyrosine Kinases, Raji E. Joseph, Lie Min, Ruo Xu, Eli D. Musselman, and Amy H. Andreotti

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Shape-dependent designability studies of lattice proteins, Myron Peto, Andrzej Kloczkowski, and Robert L. Jernigan

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Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices, Myron Peto, Taner Z. Sen, Robert L. Jernigan, and Andrzej Kloczkowski

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16-Aza-ent-beyerane and 16-Aza-ent-trachylobane:  Potent Mechanism-Based Inhibitors of Recombinant ent-Kaurene Synthase from Arabidopsis thaliana, Amab Roy, Frank G. Roberts, P. Ross Wilderman, Ke Zhou, Reuben J. Peters, and Robert M. Coates

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vGNM: a Better Model for Understanding the Dynamics of Proteins in Crystals, Guang Song and Robert L. Jernigan

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A Single Residue Switch Converts Abietadiene Synthase into a Pimaradiene Specific Cyclase, P. Ross Wilderman and Reuben J. Peters

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PIDD: database for Protein Inter-atomic Distance Distributions, Di Wu, Robert Jernigan, and Zhijun Wu

Submissions from 2006

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A mathematical model for the onset of avascular tumor growth in response to the loss of p53 function, Howard A. Levine, Michael W. Smiley, Anna L. Tucker, and Marit Nilsen-Hamilton

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Functional clustering of yeast proteins from the protein-protein interaction network, Taner Z. Sen, Andrzej Kloczkowski, and Robert L. Jernigan

Submissions from 2005

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Prediction of protein secondary structure by mining structural fragment database, Haitao Cheng, Taner Z. Sen, Andrzej Kloczkowski, Dimitris Margaritis, and Robert L. Jernigan

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Protein Promiscuity: Drug Resistance and Native Functions—HIV-1 Case, Ariel Fernandez, Dan S. Tawfik, Ben Berkhout, Rogier W. Sanders, Andrzej Kloczkowski, Taner Z. Sen, and Robert L. Jernigan

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How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?, Sanzo Miyazawa and Robert L. Jernigan