[1] Inversion methods are often used to estimate surface CO2 fluxes from atmospheric CO2 concentration measurements, given an atmospheric transport model to relate the two. The published estimates...
Knox, Maggie, Moreau, Carol, Lipscombe, James, Baker, David, Ellis, Noel
Abstract Background Dense genetic maps, together with the efficiency and accuracy of their construction, are integral to genetic studies and marker assisted selection for plant breeding....
Baker, David; Université Pierre Et Marie Curie; David.baker@etu.upmc.fr, Yor, Marc; Université Pierre Et Marie Curie; Deaproba@proba.jussieu.fr
We construct a martingale which has the same marginals as the arithmetic average of geometric Brownian motion.This provides a short proof of the recent result due to P. Carr et al that the arithmetic...
The nature of antimatter is examined in the context of algebraic quantum field theory. It is shown that the notion of antimatter is more general than that of antiparticles. Properly speaking, then,...
Assessment of the optimization of affinity and specificity at protein-DNA interfaces (2009)
Ashworth, Justin, Baker, David
The biological functions of DNA-binding proteins often require that they interact with their targets with high affinity and/or high specificity. Here, we describe a computational method that...
Structure similarity measure with penalty for close non-equivalent residues (2009)
Sadreyev, Ruslan I., Shi, ShuoYong, Baker, David, Grishin, Nick V.
Motivation:Recent improvement in homology-based structure modeling emphasizes the importance of sensitive evaluation measures that help identify and correct modest distortions in models compared with...
What a waste – an analysis of household expenditure on food (2009)
David Baker, Josh Fear, Richard Denniss
Australian households are throwing out more than $5 billion worth of food each year, more than Australians spend on digital equipment, and more than it costs to run the Australian Army. In addition...
638 REVIEW Progress in Modeling of Protein Structures and Interactions (2008)
Ora Schueler-furman, Chu Wang, Phil Bradley, Kira Misura, David Baker
The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the...
Lars Malmström, Michael Riffle, Dylan Chivian, Trisha N. Davis, Richard Bonneau, ...
Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into...
PRODUCTION AND OPERATIONS (2008)
Do More, Sell More, Contributing Writers, David Baker, Karen Bannan, David Baum, ...
POLICING OF PUBLIC DISORDER: NEW "OFFENDERS", NEW POLICING (2008)
Public disorder can become manifest in many forms: political, industrial, environmental, racial, sporting, festive and various eclectic combinations. In accommodating protest and dissent, the...
A Geometric Filter for Unbound Protein-Protein Docking ∗ (2008)
Peter Lloyd, Guillermo Sapiro, David Baker
Keywords: Protein-protein docking, geometric filtering, protein holes, statistical filtering, inter quartile range.
The nature of antimatter is examined in the context of algebraic quantum field theory. It is shown that the notion of antimatter is more general than that of antiparticles. Properly speaking, then,...
Describes setting up video game hardware for circulation at an academic library.
Describes the setup of video game hardware for circulation at an academic library.
Describes setting up video game hardware for circulation at an academic library.
Zeidman-Karpinski, Annie, Baker, David, Nigro, Rosemary, Robare, Lori, Barth, Duncan
Describes developing and deploying a popular circulating video game collection at an academic library.
Feature Selection Methods for Improving Protein Structure Prediction with Rosetta (2008)
Ben Blum, Michael Jordan, David E. Kim, Rhiju Das, Phil Bradley, David Baker
Rosetta is one of the leading algorithms for protein structure prediction today. It is a Monte Carlo energy minimization method requiring many random restarts to find structures with low energy. In...
Automated Prediction of CASP-5 Structures Using the (2008)
Robetta Server, Dylan Chivian, David E. Kim, Lars Malmström, Philip Bradley, Timothy Robertson, ...
ABSTRACT Robetta is a fully automated protein structure prediction server that uses the Rosetta fragment-insertion method. It combines template-based and de novo structure prediction methods in an...
1364 RESEARCH ARTICLES Design of a Novel Globular Protein Fold with Atomic-Level Accuracy (2008)
Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker
A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates...
Dylan Chivian, Timothy Robertson, Richard Bonneau, David Baker, Edited Philip, E. Bourne, ...
Ab initio structure prediction seeks to predict the native conformation of a protein from the amino acid sequence alone. Such attempts are both a fundamental test of our understanding of protein...
ABSTRACT We describe predictions of the (2008)
Philip Bradley, Dylan Chivian, Jens Meiler, Carol A. Rohl, William R. Schief, ...
structures of CASP5 targets using Rosetta. The Rosetta fragment insertion protocol was used to generate models for entire target domains without detectable sequence similarity to a protein of known...
MINIREVIEW Searching for folded proteins in vitro and in silico (2008)
Understanding the sequence determinants of protein structure, stabilityand folding is critical for understanding how natural proteins have evolved and how proteins can be engineered to perform novel...
Kim T. Simons, Rich Bonneau, Ingo Ruczinski, David Baker
ABSTRACT To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar...
de Novo Structure Prediction (2008)
K. V. Holmes, In Fields Virology, P. M. Howley, X. Xiao, S. Chakraborti, ...
(2001). 13. W. Li et al., Nature 426, 450 (2003). 14. H. Hofmann et al., Proc. Natl. Acad. Sci. U.S.A. 102, 7988 (2005).
Jason W. O’neill, David E. Kim, Keyji Johnsen, David Baker
monomer’s domain or secondary-structural elements, which are replaced by an identical domain from another molecule to form a dimer or oligomer [1, 2]. Domain swapping has been proposed as a...
Recapitulation and Design of Protein Binding Peptide Structures and Sequences (2008)
The recognition of short, linear peptide sequences by receptor proteins is central to many essential cellular processes, such as signalling, regulation, and the formation of protein
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and (2008)
Side-chain Conformations, Jeffrey J. Gray, Stewart Moughon, Chu Wang, Ora Schueler-furman, Brian Kuhlman, ...
The protein docking problem, that is, the task of assembling two separate protein components into their biologically relevant complex structure, is important for several reasons. First, it is of...
Center of Excellence and Departments of Medical (2008)
Oscar Millet, Anthony Mittermaier, David Baker, Lewis E. Kay, Genetics Biochemistry
The structural and dynamic properties of proteins are determined by their primary amino acid sequence. Elucidation of the rules that govern this relationship is of immense practical and
Ora Schueler-furman, Chu Wang, David Baker
Carlo minimization (MCM) on both rigid-body and side-chain degrees of freedom to identify the lowest free energy docked arrangement of 2 protein structures. An improved version of the method that...
David Baker, Simon Cox, Jon Hillier, Mark Mckeown, Ron Fowler
We have, over the past eighteen months, been developing a software toolkit to enable the sites participating in the UK e-Science Grid to carry out operational monitoring of Grid resources and to...
folding free energy landscapes using computational protein design
Feature Selection Methods for Improving Protein Structure Prediction with Rosetta (2008)
Ben Blum, Michael Jordan, David E. Kim, Rhiju Das, Philip Bradley, David Baker
Rosetta is one of the leading algorithms for protein structure prediction today. It is a Monte Carlo energy minimization method requiring many random restarts to find structures with low energy. In...
Against Field Interpretations of Quantum Field Theory (2008)
I examine some problems standing in the way of a successful ``field interpretation'' of quantum field theory. The most popular extant proposal depends on the Hilbert space of ``wavefunctionals.'' But...
Against Field Interpretations of Quantum Field Theory (2008)
I examine some problems standing in the way of a successful ``field interpretation'' of quantum field theory. The most popular extant proposal depends on the Hilbert space of ``wavefunctionals.'' But...
We construct a martingale which has the same marginals as the arithmetic average of geometric Brownian motion. This provides a short proof of the recent result due to P. Carr et al [5] that the...
We construct a martingale which has the same marginals as the arithmetic average of geometric Brownian motion. This provides a short proof of the recent result due to P. Carr et al [5] that the...
Cho, Hyundae D., Sood, Vanita D., Baker, David, Weiner, Alan M.
Archaeal class I CCA-adding enzymes use a ribonucleoprotein template to build and repair the universally conserved 3′-terminal CCA sequence of the acceptor stem of all tRNAs. A wealth of structural...
JMB---MS 665 Cust. Ref. No. FC 19/95 [SGML] (2007)
Mol Biol Recurring, Karen F. Han, David Baker, J. Mol Biol
this paper is a first step towards correlating local sequence patterns with local structural motifs
Lars Malmström, Michael Riffle, Dylan Chivian, Trisha N. Davis, Richard Bonneau, ...
Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into...
Cooperative hydrogen bonding in amyloid formation (2007)
Tsemekhman, Kiril, Goldschmidt, Lukasz, Eisenberg, David, Baker, David
Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One...
Carey, Dianne L., Baker, David, Rogers, Gary D., Petoumenos, Kathy, Chuah, John, Easey, Nicole, ...
Yes
Cooperative hydrogen bonding in amyloid formation (2007)
Tsemekhman, Kiril, Goldschmidt, Lukasz, Eisenberg, David, Baker, David
Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One...
Although historically there was no formal policy of repressing strikers, police in Australia usually responded swiftly and aggressively to employer demands to quell industrial unrest and thereby...
Prediction of structures of multidomain proteins from structures of the individual domains (2007)
Wollacott, Andrew M., Zanghellini, Alexandre, Murphy, Paul, Baker, David
We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the...
Cooperative hydrogen bonding in amyloid formation (2007)
Tsemekhman, Kiril, Goldschmidt, Lukasz, Eisenberg, David, Baker, David
Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One...
Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density (2006)
Matthew L. Baker, Wen Jiang, William J. Wedemeyer, Frazer J. Rixon, David Baker, Wah Chiu
Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy...
Sprague, Elizabeth R., Wang, Chu, Baker, David, Bjorkman, Pamela J.
Herpes simplex virus type-1 expresses a heterodimeric Fc receptor, gE-gI, on the surfaces of virions and infected cells that binds the Fc region of host immunoglobulin G and is implicated in the...
Elizabeth R. Sprague, Chu Wang, David Baker, Pamela J. Bjorkman
Herpes simplex virus type-1 expresses a heterodimeric Fc receptor, gE-gI, on the surfaces of virions and infected cells that binds the Fc region of host immunoglobulin G and is implicated in the...
Access the most recent version at doi: 10.1110/ps.062353106 References (2006)
Re Zanghellini, Lin Jiang, Andrew M. Wollacott, Gong Cheng, Jens Meiler, Eric A. Althoff, ...
New algorithms and an in silico benchmark for computational
Re Zanghellini, Lin Jiang, Andrew M. Wollacott, Gong Cheng, Jens Meiler, Eric A. Althoff, ...
New algorithms and an in silico benchmark for computational
The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a...
Prediction of structures of multidomain proteins from structures of the individual domains (2006)
Wollacott, Andrew M., Zanghellini, Alexandre, Murphy, Paul, Baker, David
We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the...
New algorithms and an in silico benchmark for computational enzyme design (2006)
Zanghellini, Alexandre, Jiang, Lin, Wollacott, Andrew M., Cheng, Gong, Meiler, Jens, Althoff, Eric A., ...
The creation of novel enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Here we describe two new algorithms for enzyme design that...
The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a...
Prediction of structures of multidomain proteins from structures of the individual domains (2006)
Wollacott, Andrew M., Zanghellini, Alexandre, Murphy, Paul, Baker, David
We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the...
The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a...
Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker
ABSTRACT Water-mediated hydrogen bonds play critical roles at protein–protein and protein– nucleic acid interfaces, and the interactions formed by discrete water molecules cannot be captured...
Recapitulation of protein family divergence using flexible backbone protein design (2005)
Christopher T. Saunders, David Baker, Howard Hughes Medical
The evolution of protein families is subject to numerous constraints unified by a simple necessity: the preservation and elaboration of biological function. To represent this evolutionary process a
Progress and challenges in high-resolution refinement of protein structure models (2005)
ABSTRACT Achieving atomic level accuracy in de novo structure prediction presents a formidable challenge even in the context of protein models with correct topologies. High-resolution refinement is a...
Protein-DNA binding specificity predictions with structural models (2005)
Re V. Morozov, James J. Havranek, David Baker, Eric D. Siggia
Protein–DNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in protein–DNA complexes...
Electron Density Redistribution Accounts for Half the Cooperativity of r Helix Formation (2005)
Re V. Morozov, Kiril Tsemekhman, David Baker
The energy of R helix formation is well known to be highly cooperative, but the origin and relative importance of the contributions to helical cooperativity have been unclear. Here we separate the...
Improved side-chain modeling for protein-protein docking (2005)
Chu Wang, Ora Schueler-furman, David Baker
Success in high-resolution protein–protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations...
Improved side-chain modeling for protein-protein docking (2005)
Wang, Chu, Schueler-Furman, Ora, Baker, David
Success in high-resolution protein–protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations...
Britain and Europe: The Dog that Didn't Bark (2005)
Baker, David, Sherrington, Philippa
2004 was a busy and arguably historic year for the EU. It saw the enlargement of its membership to 25, the long-awaited agreement on the new EU constitution, and EP elections. Tony Blair persisted in...
Protein-DNA binding specificity predictions with structural models (2005)
Morozov, Alexandre V., Havranek, James J., Baker, David, Siggia, Eric D.
Protein–DNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in protein–DNA complexes...
Cheng, Gong, Qian, Bin, Samudrala, Ram, Baker, David
The prediction of functional sites in newly solved protein structures is a challenge for computational structural biology. Most methods for approaching this problem use evolutionary conservation as...
Wasteful consumption in Australia (2005)
Clive Hamilton, Richard Denniss, David Baker
If government programs aimed at reducing waste are to achieve their stated goal then they cannot continue to avoid the nexus between growing waste generation and rising consumption expenditure, argue...
Wasteful consumption in Australia (2005)
Clive Hamilton, Richard Denniss, David Baker
If government programs aimed at reducing waste are to achieve their stated goal then they cannot continue to avoid the nexus between growing waste generation and rising consumption expenditure, argue...
Qian, Bin, Ortíz, Angel R., Baker, David
Accurate high-resolution refinement of protein structure models is a formidable challenge because of the delicate balance of forces in the native state, the difficulty in sampling the very large...
Carr, A., Workman, C., Carey, D., Rogers, G. D., Martin, A., Baker, David, ...
Copyright © 2004 Elsevier Ltd All rights reserved.
Carr, A., Workman, C., Carey, D., Rogers, G. D., Martin, A., Baker, David, ...
Copyright © 2004 Elsevier Ltd All rights reserved.
Access the most recent version at doi: 10.1110/ps.041222905 References (2004)
Chu Wang, Ora Schueler-furman, David Baker, Email Alerting, Chu Wang, Ora Schueler-furman, ...
service
Michelle Scalley-kim, David Baker, Howard Hughes Medical
Over the past 15 years the protein folding field has been revolutionized by the acquisition of experimental data on the folding of a large number of small, single domain proteins with much simpler
D: Strand-loop-strand motifs: Prediction of hairpins and diverging turns in proteins (2004)
Michael Kuhn, Jens Meiler, David Baker
ABSTRACT �-sheet proteins have been particularly challenging for de novo structure prediction methods, which tend to pair adjacent �-strands into �-hairpins and produce overly local topologies....
Protein structure prediction and analysis using the Robetta server (2004)
David E. Kim, Dylan Chivian, David Baker
The Robetta server
Modeling structurally variable regions in homologous proteins with rosetta (2004)
Carol A. Rohl, Dylan Chivian, David Baker
ABSTRACT A major limitation of current comparative modeling methods is the accuracy with which regions that are structurally divergent from homologues of known structure can be modeled. Because...
Abstract Communication The fumarate sensor DcuS (2004)
progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy
A simple physical model for the prediction and design of protein–DNA interactions (2004)
James J. Havranek, Carlos M. Duarte, David Baker, Howard Hughes Medical
Protein–DNA interactions are crucial for many biological processes. Attempts to model these interactions have generally taken the form of amino acid–base recognition codes or purely...
Protein structure prediction and analysis using the Robetta server (2004)
Kim, David E., Chivian, Dylan, Baker, David
The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into...
Britain and Europe: Europe and/or America? (2004)
Baker, David, Sherrington, Philippa
Government policy on Iraq meant a tense year for Labour. International politics dominated in the early months of 2003 and Blair's preference for Atlanticism had a corrosive effect upon European...
Chen, Yu, Kortemme, Tanja, Robertson, Tim, Baker, David, Varani, Gabriele
RNA-binding proteins play many essential roles in the regulation of gene expression in the cell. Despite the significant increase in the number of structures for RNA–protein complexes in the last...
Schlosshauer, Maximilian, Baker, David
We develop a simple but rigorous model of protein–protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding...
Schlosshauer, Maximilian, Baker, David
We develop a simple but rigorous model of protein–protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding...
This study investigates how four urban school districts, serving low socioeconomic status (SES) student populations, define, prepare teachers for, and implement integration of computer technology...
This study investigates how four urban school districts, serving low socioeconomic status (SES) student populations, define, prepare teachers for, and implement integration of computer technology...
"The Shotgun Marriage: Managing Eurosceptical Opinion in British Political Parties 1972-2002" (2003)
In party management terms European Union represents a clear case of an uncomfortable political ‘shotgun marriage’, in the sense that UK party leaders and their managers have to deal with an...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Of unprincipled formalism readings in the work of David Malouf and Peter Carey (2003)
Facsimile of the author's original dissertation. Pagination of document: vi, 270 leaves. Includes bibliographical references. Abstract: This thesis develops a critical reading methodology entitled...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Access the most recent version at doi: 10.1110/ps.03197403 References (2003)
Ruslan I. Sadreyev, David Baker, Nick V. Grishin, Email Alerting, Ruslan I. Sadreyev, David Baker, ...
homologies between protein families
Building the e-Science Grid in the UK: Middleware, Applications and Tools (2003)
Deployed At Level, Rob Allan, David Baker, David Boyd, Dharmesh Chohan, Simon Cox, ...
Over the period September 2002-April 2003 the UK Grid Engineering Task Force and staff at Regional eScience Centres and CCLRC deployed the Globus Toolkit GT2 at 14 sites and on approximately 80...
William J. Wedemeyer, David Baker
ABSTRACT Angular potentials play an important role in the refinement of protein structures through angle-dependent restraints (e.g., those determined by cross-correlated relaxations, residual dipolar...
Henrik G. Svensson, William J. Wedemeyer, Jennifer L. Ekstrom, David R. Callender, Tanja Kortemme, David E. Kim, ...
ABSTRACT: Protein L is a bacterial surface protein with 4-5 immunoglobulin (Ig)-binding domains (B1-B5), each of which appears to have two binding sites for Ig, corresponding to the two edges of its...
Gautam Dantas, Brian Kuhlman, David Callender, Michelle Wong, David Baker, Howard Hughes Medical
The ultimate goal of protein design is the creation of novel proteins that perform specified tasks. A necessary requirement for meeting this goal is the ability to identify sequences that fold
Contact order revisited: influence of protein size on the folding rate. Protein Sci (2003)
Dmitry N. Ivankov, Sergiy O. Garbuzynskiy, Eric Alm, Kevin W. Plaxco, David Baker, Alexei V. Finkelstein
Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical...
Jerry Tsai, Richard Bonneau, Re V. Morozov, Brian Kuhlman, Carol A. Rohl, David Baker
ABSTRACT We have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on sidechains and minimizing...
Structural and kinetic characterization of the simplified SH3 domain FP1. Protein Sci (2003)
Qian Yi, Ponni Rajagopal, Rachel E. Klevit, David Baker
The simplified SH3 domain sequence, FP1, obtained in phage display selection experiments has an amino acid composition that is 95 % Ile, Lys, Glu, Ala, Gly. Here we use NMR to investigate the...
Protein-protein docking predictions for the CAPRI experiment (2003)
Jeffrey J. Gray, Stewart E. Moughon, Tanja Kortemme, Ora Schueler-furman, Re V. Morozov, ...
ABSTRACT We predicted structures for all seven targets in the CAPRI experiment using a new method in development at the time of the challenge. The technique includes a low-resolution rigid body Monte...
Evaluation of models of electrostatic interactions in proteins (2003)
Re V. Morozov, Tanja Kortemme, David Baker
The conformations of proteins and protein-protein complexes observed in nature must be low in free energy relative to alternative (not observed) conformations, and it is plausible (but not absolutely...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Britain and Europe: Treading Water or Slowly Drowning? (2003)
Little appeared to have changed in Britain's relations with Europe in 2002: speculation about the Britain joining the euro continued; euroscepticism continued to operate at a low key; and Britain...
Structural and kinetic characterization of the simplified SH3 domain FP1 (2003)
Yi, Qian, Rajagopal, Ponni, Klevit, Rachel E., Baker, David
The simplified SH3 domain sequence, FP1, obtained in phage display selection experiments has an amino acid composition that is 95% Ile, Lys, Glu, Ala, Gly. Here we use NMR to investigate the tertiary...
Cannabinoids inhibit neurodegeneration in models of multiple sclerosis (2003)
Pryce, Gareth, Ahmed, Zubair, Hankey, Deborah J. R., Jackson, Samuel J., Croxford, J. Ludovic, Pocock, Jennifer M., ...
Multiple sclerosis is increasingly being recognized as a neurodegenerative disease that is triggered by inflammatory attack of the CNS. As yet there is no satisfactory treatment. Using experimental...
Profile-profile comparisons by COMPASS predict intricate homologies between protein families (2003)
Sadreyev, Ruslan I., Baker, David, Grishin, Nick V.
Recently we proposed a novel method of alignment–alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present...
Low free energy cost of very long loop insertions in proteins (2003)
Scalley-Kim, Michelle, Minard, Philippe, Baker, David
Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded...
Contact order revisited: Influence of protein size on the folding rate (2003)
Ivankov, Dmitry N., Garbuzynskiy, Sergiy O., Alm, Eric, Plaxco, Kevin W., Baker, David, Finkelstein, Alexei V.
Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical...
Cannabinoids inhibit neurodegeneration in models of multiple sclerosis (2003)
Pryce, Gareth, Ahmed, Zubair, Hankey, Deborah J. R., Jackson, Samuel J., Croxford, J. Ludovic, Pocock, Jennifer M., ...
Multiple sclerosis is increasingly being recognized as a neurodegenerative disease that is triggered by inflammatory attack of the CNS. As yet there is no satisfactory treatment. Using experimental...
Of Unprincipled Formalism: Readings in the Work of David Malouf and Peter Carey (2003)
This thesis develops a critical reading methodology entitled unprincipled formalism. This methodology is tested in close readings of three relatively contemporary Australian literary texts: David...
Lectio divina : toward a psychology of contemplation / (2002)
Thesis (Ph. D.)--Pacifica Graduate Institute, 2002.
A general expression for bimolecular association rates with orientational constraints (2002)
Maximilian Schlosshauer, David Baker
We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur...
Evaluation of structural and evolutionary contributions to deleterious mutation prediction (2002)
Christopher T. Saunders, David Baker, Howard Hughes Medical
The rapid discovery of single nucleotide polymorphisms (SNP) in the human genome has created an opportunity for high-throughput deleterious mutation prediction methods to discover
Design, activity, and structure of a highly specific artificial endonuclease (2002)
Brett S. Chevalier, Tanja Kortemme, Meggen S. Chadsey, David Baker, Raymond J. Monnat
We have generated an artificial highly specific endonuclease by fusing domains of homing endonucleases 2 I-DmoI and I-CreI and creating a new 1400 A ˚ protein interface between these domains....
Stefan M. Larson, Ingo Ruczinski, Alan R. Davidson, David Baker, Kevin W. Plaxco, Howard Hughes Medical
*Corresponding authors Abbreviations used: ACBP, acylcarrier binding protein; AcP, acylphosphatase; ADA2h, the activation domain of human carboxypeptidase; CI2, chymotrypsin inhibitor 2; FKBP, FK506...
Simple physical models connect theory and experiments in protein folding kinetics (2002)
Eric Alm, Re V. Morozov, Tanja Kortemme, David Baker, Howard Hughes Medical
Recent theoretical models by Alm & Baker, 1
Accurate computer-based design of a new backbone conformation in the second turn of protein (2002)
Brian Kuhlman, Jason W. O'neill, David E. Kim, David Baker
*Corresponding authors
Crystal structures and increased stabilization of the protein G (2002)
Ronald E. Stenkamp, David Teller, David Baker
variants with switched folding pathways
ACCELERATED COMMUNICATION Low free energy cost of very long loop insertions in proteins (2002)
Michelle Scalley-kim, Philippe Minard, David Baker
Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded...
De novo prediction of three-dimensional structures for major protein families (2002)
Richard Bonneau, Carol A. Rohl, Dylan Chivian, Phillip Bradley, Lars Malmström, ...
As the number of gene sequences in databases, public and private, increase dramatically, so do the number of genes of unknown function. Of the protein sequences currently available approximately
Nauli, Sehat, Kuhlman, Brian, Le Trong, Isolde, Stenkamp, Ronald E., Teller, David, Baker, David
We recently described two protein G variants (NuG1 and NuG2) with redesigned first hairpins that were almost twice as stable, folded 100-fold faster, and had a switched folding mechanism relative to...
Contact order and ab initio protein structure prediction (2002)
Bonneau, Richard, Ruczinski, Ingo, Tsai, Jerry, Baker, David
Although much of the motivation for experimental studies of protein folding is to obtain insights for improving protein structure prediction, there has been relatively little connection between...
Contact order and ab initio protein structure prediction (2001)
Downloaded From, Richard Bonneau, Ingo Ruczinski, Jerry Tsai, David Baker, Email Alerting, ...
service
Philippe Minard, Michelle Scalley-kim, Alex Watters, David Baker
amino acid sequences
Circularization changes the folding transition state of the src SH3 domain (2001)
Viara P. Grantcharova, David Baker
A recent development in the protein folding ®eld has been the empirical observation that native state topology is a major determinant of folding rates, with simple fold proteins folding faster than
Functional Inferences from Blind ab Initio Protein (2001)
Structure Predictions Richard, Richard Bonneau, Jerry Tsai, Ingo Ruczinski, David Baker
this report we illustrate how ab initio protein structure prediction can potentially contribute to genome annotation using as examples several of our blind protein structure predictions from CASP3...
Prospects for ab initio protein structural genomics (2001)
Kim T. Simons, Charlie Strauss, David Baker
Protein sequences are being determined at a rate faster than the solutions of their three-dimensional structures. As structural information is critical to our understanding of the basis of the...
Molecular dynamics in the endgame of protein structure prediction (2001)
Matthew R. Lee, Jerry Tsai, David Baker, Peter A. Kollman
Approaches for predicting three-dimensional protein structure based on amino acid sequence, ranging from ab initio to comparative modeling, all make considerable approximations in order to contend
Protein structure prediction and structural genomics (2001)
Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although...
A ``loop entropy reduction'' phage-display selection for folded amino acid sequences (2001)
Minard, Philippe, Scalley-Kim, Michelle, Watters, Alex, Baker, David
As a step toward selecting folded proteins from libraries of randomized sequences, we have designed a `loop entropy reduction'-based phage-display method. The basic premise is that insertion of a...
Panelism in Action: Labour’s 1999 European Parliamentary candidate selections (2000)
Wring, Dominic, Baker, David, Seawright, David
This article was published in Political Quarterly [© Blackwell]. The definitive version is available at: http://www.blackwell-synergy.com/loi/poqu.
Hmmstr: a hidden markov model for local sequence-structure correlations in proteins (2000)
Christopher Bystroff, Vesteinn Thorsson, David Baker
*Corresponding authors
Edward C. Thayer, Chris Bystroff, David Baker
Locating protein coding regions in genomic DNA is a critical step in accessing the information generated by large scale sequencing projects. Current methods for gene detection depend on statistical...
NMR characterization of residual structure in the denatured state of protein (2000)
Qian Yi, Eric J. Alm, David Baker
How a protein folds into a unique three-dimensional structure is one of the greatest questions of modern structural biology. An exciting recent development is the direct structural characterization
Edward C. Thayer, Chris Bystroff, David Baker
Locating protein coding regions in genomic DNA is a critical step in accessing the information generated by large scale sequencing projects. Current methods for gene detection depend on statistical...
A breakdown of symmetry in the folding transition state of protein (2000)
David E. Kim, Cindy Fisher, David Baker
Understanding the folding mechanisms of small proteins which fold without well populated intermediates requires the determination of the distribution of structure in the folding transition state
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding (1999)
Jerry Tsai, Michael Levitt, David Baker
Molecular dynamics (MD) simulations provide a means to obtain atomic level views of protein unfolding not accessible to direct experimental measurement (Brooks, 1998). Despite inaccuracies
Structural transitions in the protein L denatured state ensemble (1999)
Michelle L. Scalley, Sehat Nauli, Sharon T. Gladwin, David Baker
ABSTRACT: We use a broad array of biophysical methods to probe the extent of structure and time scale of structural transitions in the protein L denatured state ensemble. Measurement of amide proton...
H. Gu, N. Doshi, D. E. Kim, K. T. Simons, J. V. Santiago, S. Nauli, ...
We use both combinatorial and site-directed mutagenesis to explore the consequences of surface hydrophobic substitutions for the folding of two small single domain proteins, the src SH3 domain, and...
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding (1999)
Jerry Tsai, Michael Levitt, David Baker
Molecular dynamics (MD) simulations provide a means to obtain atomic level views of protein unfolding not accessible to direct experimental measurement (Brooks, 1998). Despite inaccuracies
Kim T. Simons, Ingo Ruczinski, Charles Kooperberg, Brian A. Fox, Chris Bystroff, David Baker
ABSTRACT We describe the development of a scoring function based on the decomposition P(structure0sequence) � P(sequence0structure) *P(structure), which outperforms previous scoring functions in...
Kim T. Simons, Ingo Ruczinski, Charles Kooperberg, Brian A. Fox, Chris Bystroff, David Baker
ABSTRACT We describe the development of a scoring function based on the decomposition P(structure0sequence) � P(sequence0structure) *P(structure), which outperforms previous scoring functions in...
Qian Yi, Chris Bystroff, Ponni Rajagopal, Rachel E. Klevit, David Baker
There has been considerable discussion about the role of local interactions in protein folding
Prediction of local structure in proteins using a library of sequence-structure motifs (1998)
Christopher Bystroff, David Baker
*Corresponding authors
Qian Yi, Chris Bystroff, Ponni Rajagopal, Rachel E. Klevit, David Baker
There has been considerable discussion about the role of local interactions in protein folding
The single helix in protein L is largely disrupted at the rate-limiting step in folding (1998)
David E. Kim, Qian Yi, Sharon T. Gladwin, Jonathan M. Goldberg, David Baker
The role of helix formation in the folding of small proteins has been the subject of considerable
FOR THE RECORD Three-dimensional structures and contexts associated (1997)
Email Alerting, Karen E Han, Christopher Bystroff, David Baker
Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns
Blind predictions of local protein structure in casp2 targets using the i-sites library (1997)
Christopher Bystroff, David Baker
ABSTRACT Blind predictions of the local structure of nine CASP2 targets were made using the I-sites library of short sequence— structure motifs, revealing strengths and weaknesses in this new...
Folding dynamics of the src SH3 domain (1997)
Viara P. Grantcharova, David Baker
using equilibrium and stopped-flow fluorescence, circular dichroism (CD), and nuclear magnetic resonance (NMR) hydrogen exchange experiments. As found for other SH3 domains, guanidinium chloride...
Jack D. Sobel, Walter Chaim, Jessica Thomason, Charles Livengood, Richard Sweet, James A. McGregor, ...
Objective: We sought to compare the efficacy of metronidazole gel vs. triple-sulfa cream in the treatment of bacterial vaginosis (BV).Methods: In a double-blinded study, 247 women with symptomatic BV...
Typescript.
Mack, Kathy, Lucke, H. K., Baker, David, Stewart, Andrew
Cases and materials on evidence by P.K. Waight and C.R. Williams, reviewed by Kathy Mack. Statutes by I.A. MacAdam and T.M. Smith, reviewed by Kathy Mack. Bibliography of legal Festschriften, titles...
Mack, Kathy, Lucke, H. K., Baker, David, Stewart, Andrew
Cases and materials on evidence by P.K. Waight and C.R. Williams, reviewed by Kathy Mack. Statutes by I.A. MacAdam and T.M. Smith, reviewed by Kathy Mack. Bibliography of legal Festschriften, titles...
Stewart, A. J., Castles, A. C., Crawford, J., McEvoy, K. P., Baker, David, Goode, M., ...
The High Court of Australia on contract 1950-1980 by M.P. Ellinghaus, reviewed by A.J. Stewart. Reform the Law, essays on the renewal of the Australian legal system by Michael Kirby, reviewed by A.C....
Stewart, A. J., Castles, A. C., Crawford, J., McEvoy, K. P., Baker, David, Goode, M., ...
The High Court of Australia on contract 1950-1980 by M.P. Ellinghaus, reviewed by A.J. Stewart. Reform the Law, essays on the renewal of the Australian legal system by Michael Kirby, reviewed by A.C....
Baker, David, Keeler, John, McEvoy, K. P., Churches, Steven, Elliott Jacqueline
Cases on torts by W.L. Morison and others, Torts cases and commentary by H. Luntz, D. Hambly and P. Hayes, reviewed by David Baker. Negligence and economic torts: selected aspects edited by T. Simos,...
Baker, David, Keeler, John, McEvoy, K. P., Churches, Steven, Elliott Jacqueline
Cases on torts by W.L. Morison and others, Torts cases and commentary by H. Luntz, D. Hambly and P. Hayes, reviewed by David Baker. Negligence and economic torts: selected aspects edited by T. Simos,...
Root sucker and stem sprout regrowth on clearcut aspen sites. (1973)
http://deepblue.lib.umich.edu/bitstream/2027.42/52681/1/1114.pdf
Contact order and ab initio protein structure prediction. Protein Sci 2002;11:1937 (1937)
Richard Bonneau, Ingo Ruczinski, Jerry Tsai, David Baker
Although much of the motivation for experimental studies of protein folding is to obtain insights for improving protein structure prediction, there has been relatively little connection between...
Stankunas, Kryn, Bayle, J. Henri, Havranek, James J., Wandless, Thomas J., Baker, David, Crabtree, Gerald R., ...
We recently reported that certain mutations in the FK506-rapamycin binding (FRB) domain disrupt its stability in vitro and in vivo (Stankunas et al. Mol. Cell , 2003 , 12 , 1615). To determine the...
Cooperative hydrogen bonding in amyloid formation
Tsemekhman, Kiril, Goldschmidt, Lukasz, Eisenberg, David, Baker, David
Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One...
Improved side-chain modeling for protein–protein docking
Wang, Chu, Schueler-Furman, Ora, Baker, David
Success in high-resolution protein–protein docking requires accurate modeling of side-chain conformations at the interface. Most current methods either leave side chains fixed in the conformations...
Schlosshauer, Maximilian, Baker, David
We develop a simple but rigorous model of protein–protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding...
Prediction of the structure of symmetrical protein assemblies
André, Ingemar, Bradley, Philip, Wang, Chu, Baker, David
Biological supramolecular systems are commonly built up by the self-assembly of identical protein subunits to produce symmetrical oligomers with cyclical, icosahedral, or helical symmetry that play...
Low free energy cost of very long loop insertions in proteins
Scalley-Kim, Michelle, Minard, Philippe, Baker, David
Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded...
Structural and kinetic characterization of the simplified SH3 domain FP1
Yi, Qian, Rajagopal, Ponni, Klevit, Rachel E., Baker, David
The simplified SH3 domain sequence, FP1, obtained in phage display selection experiments has an amino acid composition that is 95% Ile, Lys, Glu, Ala, Gly. Here we use NMR to investigate the tertiary...
Contact order revisited: Influence of protein size on the folding rate
Ivankov, Dmitry N., Garbuzynskiy, Sergiy O., Alm, Eric, Plaxco, Kevin W., Baker, David, Finkelstein, Alexei V.
Guided by the recent success of empirical model predicting the folding rates of small two-state folding proteins from the relative contact order (CO) of their native structures, by a theoretical...
Profile–profile comparisons by COMPASS predict intricate homologies between protein families
Sadreyev, Ruslan I., Baker, David, Grishin, Nick V.
Recently we proposed a novel method of alignment–alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present...
Comparative Study of Intravaginal Metronidazole and Triple-Sulfa Therapy for Bacterial Vaginosis
Sobel, Jack D., Chaim, Walter, Thomason, Jessica, Livengood, Charles, Sweet, Richard, McGregor, James A., ...
Objective: We sought to compare the efficacy of metronidazole gel vs. triple-sulfa cream in the treatment of bacterial vaginosis (BV).
A ``loop entropy reduction'' phage-display selection for folded amino acid sequences
Minard, Philippe, Scalley-Kim, Michelle, Watters, Alex, Baker, David
As a step toward selecting folded proteins from libraries of randomized sequences, we have designed a `loop entropy reduction'-based phage-display method. The basic premise is that insertion of a...
Contact order and ab initio protein structure prediction
Bonneau, Richard, Ruczinski, Ingo, Tsai, Jerry, Baker, David
Although much of the motivation for experimental studies of protein folding is to obtain insights for improving protein structure prediction, there has been relatively little connection between...
Nauli, Sehat, Kuhlman, Brian, Le Trong, Isolde, Stenkamp, Ronald E., Teller, David, Baker, David
We recently described two protein G variants (NuG1 and NuG2) with redesigned first hairpins that were almost twice as stable, folded 100-fold faster, and had a switched folding mechanism relative to...
Consistent blind protein structure generation from NMR chemical shift data
Shen, Yang, Lange, Oliver, Delaglio, Frank, Rossi, Paolo, Aramini, James M., Liu, Gaohua, ...
Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for de novo protein structure generation, using as input experimental...
Structural inference of native and partially folded RNA by high-throughput contact mapping
Das, Rhiju, Kudaravalli, Madhuri, Jonikas, Magdalena, Laederach, Alain, Fong, Robert, Schwans, Jason P., ...
The biological behaviors of ribozymes, riboswitches, and numerous other functional RNA molecules are critically dependent on their tertiary folding and their ability to sample multiple functional...
Cho, Hyundae D., Sood, Vanita D., Baker, David, Weiner, Alan M.
Archaeal class I CCA-adding enzymes use a ribonucleoprotein template to build and repair the universally conserved 3′-terminal CCA sequence of the acceptor stem of all tRNAs. A wealth of structural...
Prospects for de novo phasing with de novo protein models
In a first systematic exploration of phasing with Rosetta de novo models, it is shown that all-atom refinement of coarse-grained models significantly improves both the model quality and performance...
Emergence of symmetry in homooligomeric biological assemblies
André, Ingemar, Strauss, Charlie E. M., Kaplan, David B., Bradley, Philip, Baker, David
Naturally occurring homooligomeric protein complexes exhibit striking internal symmetry. The evolutionary origins of this symmetry have been the subject of considerable speculation; proposals for the...
Estimating High Latitude Carbon Fluxes With Inversions Of Atmospheric CO2
Roger Dargaville, David Baker, Christian Rödenbeck, Peter Rayner, Philippe Ciais
Global carbon cycle, atmospheric inversions, Boreal ecosystems,
Alteration of enzyme specificity by computational loop remodeling and design
Murphy, Paul M., Bolduc, Jill M., Gallaher, Jasmine L., Stoddard, Barry L., Baker, David
Altering the specificity of an enzyme requires precise positioning of side-chain functional groups that interact with the modified groups of the new substrate. This requires not only sequence changes...
Structure similarity measure with penalty for close non-equivalent residues
Sadreyev, Ruslan I., Shi, ShuoYong, Baker, David, Grishin, Nick V.
Motivation:Recent improvement in homology-based structure modeling emphasizes the importance of sensitive evaluation measures that help identify and correct modest distortions in models compared with...
Assessment of the optimization of affinity and specificity at protein–DNA interfaces
Ashworth, Justin, Baker, David
The biological functions of DNA-binding proteins often require that they interact with their targets with high affinity and/or high specificity. Here, we describe a computational method that...
Computation of Conformational Coupling in Allosteric Proteins
Kidd, Brian A., Baker, David, Thomas, Wendy E.
In allosteric regulation, an effector molecule binding a protein at one site induces conformational changes, which alter structure and function at a distant active site. Two key challenges in the...
Clayton, T. Andrew, Baker, David, Lindon, John C., Everett, Jeremy R., Nicholson, Jeremy K.
We provide a demonstration in humans of the principle of pharmacometabonomics by showing a clear connection between an individual's metabolic phenotype, in the form of a predose urinary metabolite...
Simultaneous prediction of protein folding and docking at high resolution
Das, Rhiju, André, Ingemar, Shen, Yang, Wu, Yibing, Lemak, Alexander, Bansal, Sonal, ...
Interleaved dimers and higher order symmetric oligomers are ubiquitous in biology but present a challenge to de novo structure prediction methodology: The structure adopted by a monomer can be...