Published in Nature on September 22, 2005
Rewiring the specificity of two-component signal transduction systems. Cell (2008) 4.80
Protein sectors: evolutionary units of three-dimensional structure. Cell (2009) 3.76
MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics (2006) 2.81
Emerging methods in protein co-evolution. Nat Rev Genet (2013) 2.72
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44
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Folding versus aggregation: polypeptide conformations on competing pathways. Arch Biochem Biophys (2007) 1.97
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Requirements for efficient correction of ΔF508 CFTR revealed by analyses of evolved sequences. Cell (2012) 1.81
Protein co-evolution, co-adaptation and interactions. EMBO J (2008) 1.65
Two-component protein-engineered physical hydrogels for cell encapsulation. Proc Natl Acad Sci U S A (2009) 1.63
Pairwise maximum entropy models for studying large biological systems: when they can work and when they can't. PLoS Comput Biol (2009) 1.50
Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein. PLoS Genet (2016) 1.46
Integrated analysis of residue coevolution and protein structures capture key protein sectors in HIV-1 proteins. PLoS One (2015) 1.42
An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol (2010) 1.42
Computationally designed libraries of fluorescent proteins evaluated by preservation and diversity of function. Proc Natl Acad Sci U S A (2006) 1.38
Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Nat Struct Mol Biol (2009) 1.37
Extracting function from a beta-trefoil folding motif. Proc Natl Acad Sci U S A (2008) 1.34
Signal transduction pathway of TonB-dependent transporters. Proc Natl Acad Sci U S A (2006) 1.32
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Traceless protein splicing utilizing evolved split inteins. Proc Natl Acad Sci U S A (2009) 1.28
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Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol (2012) 1.18
Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity. Proc Natl Acad Sci U S A (2008) 1.11
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Ultra-fast evaluation of protein energies directly from sequence. PLoS Comput Biol (2006) 1.11
On side-chain conformational entropy of proteins. PLoS Comput Biol (2006) 1.05
From principal component to direct coupling analysis of coevolution in proteins: low-eigenvalue modes are needed for structure prediction. PLoS Comput Biol (2013) 1.03
Direct correlation analysis improves fold recognition. Comput Biol Chem (2011) 1.03
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Structural basis for polyproline recognition by the FE65 WW domain. J Mol Biol (2007) 1.01
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A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evol Biol (2006) 0.97
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The yeast E4 ubiquitin ligase Ufd2 interacts with the ubiquitin-like domains of Rad23 and Dsk2 via a novel and distinct ubiquitin-like binding domain. J Biol Chem (2010) 0.95
A divide-and-conquer approach to determine the Pareto frontier for optimization of protein engineering experiments. Proteins (2011) 0.94
Transition states in protein folding kinetics: modeling phi-values of small beta-sheet proteins. Biophys J (2007) 0.93
From residue coevolution to protein conformational ensembles and functional dynamics. Proc Natl Acad Sci U S A (2015) 0.92
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev (2016) 0.92
RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA (2011) 0.91
Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation. PLoS One (2010) 0.91
Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling. BMC Struct Biol (2008) 0.90
How directional translocation is regulated in a DNA helicase motor. Biophys J (2007) 0.89
Influence of hPin1 WW N-terminal domain boundaries on function, protein stability, and folding. Protein Sci (2007) 0.88
Epistasis in protein evolution. Protein Sci (2016) 0.88
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Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors. PLoS One (2009) 0.87
Trade-off between positive and negative design of protein stability: from lattice models to real proteins. PLoS Comput Biol (2009) 0.86
Optimization of combinatorial mutagenesis. J Comput Biol (2011) 0.85
Adaptable hydrogel networks with reversible linkages for tissue engineering. Adv Mater (2015) 0.85
Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Comput Biol (2016) 0.84
Protein sectors: statistical coupling analysis versus conservation. PLoS Comput Biol (2015) 0.84
Correlated mutations via regularized multinomial regression. BMC Bioinformatics (2011) 0.84
Interrogating and predicting tolerated sequence diversity in protein folds: application to E. elaterium trypsin inhibitor-II cystine-knot miniprotein. PLoS Comput Biol (2009) 0.83
Protein stability: computation, sequence statistics, and new experimental methods. Curr Opin Struct Biol (2015) 0.83
Computational identification of novel amino-acid interactions in HIV Gag via correlated evolution. PLoS One (2012) 0.83
Evolution based on domain combinations: the case of glutaredoxins. BMC Evol Biol (2009) 0.83
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps. BMC Biol (2011) 0.82
Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands. Pharmaceuticals (Basel) (2010) 0.81
Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models. PLoS Comput Biol (2016) 0.81
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Sets of covariant residues modulate the activity and thermal stability of GH1 β-glucosidases. PLoS One (2014) 0.81
Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features. PLoS One (2012) 0.80
The Context-Dependence of Mutations: A Linkage of Formalisms. PLoS Comput Biol (2016) 0.80
Fold designability, distribution, and disease. PLoS Comput Biol (2006) 0.80
Consensus protein design. Protein Eng Des Sel (2016) 0.80
Directed evolution to re-adapt a co-evolved network within an enzyme. J Biotechnol (2011) 0.80
Structure-based design of combinatorial mutagenesis libraries. Protein Sci (2015) 0.80
Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator. Chem Sci (2015) 0.79
Probing the mutational interplay between primary and promiscuous protein functions: a computational-experimental approach. PLoS Comput Biol (2012) 0.79
Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci (2012) 0.78
Correlation analysis for protein evolutionary family based on amino acid position mutations and application in PDZ domain. PLoS One (2010) 0.78
Evolution-Based Functional Decomposition of Proteins. PLoS Comput Biol (2016) 0.78
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. PLoS Comput Biol (2017) 0.77
Conserved and variable correlated mutations in the plant MADS protein network. BMC Genomics (2010) 0.77
NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucleic Acids Res (2014) 0.77
Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A. J Mol Biol (2008) 0.77
Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions. J Comput Aided Mol Des (2013) 0.76
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. PLoS Comput Biol (2016) 0.76
Functional characterisation of the WW minimal domain for delivering therapeutic proteins by adenovirus dodecahedron. PLoS One (2012) 0.76
Structure of FIV capsid C-terminal domain demonstrates lentiviral evasion of genetic fragility by coevolved substitutions. Sci Rep (2016) 0.76
Live imaging of inorganic phosphate in plants with cellular and subcellular resolution. Plant Physiol (2015) 0.76
Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software. Sci Rep (2015) 0.75
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Mol Biol Evol (2017) 0.75
Crystallization and preliminary X-ray crystallographic analysis of an artificial molten-globular-like triosephosphate isomerase protein of mixed phylogenetic origin. Acta Crystallogr F Struct Biol Commun (2014) 0.75
Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol (2003) 6.50
Structural basis of a phototropin light switch. Science (2003) 5.09
Protein sectors: evolutionary units of three-dimensional structure. Cell (2009) 3.76
Structural determinants of allosteric ligand activation in RXR heterodimers. Cell (2004) 3.36
CFTR channel opening by ATP-driven tight dimerization of its nucleotide-binding domains. Nature (2005) 3.24
White collar-1, a DNA binding transcription factor and a light sensor. Science (2002) 2.97
Surface sites for engineering allosteric control in proteins. Science (2008) 2.82
Natural-like function in artificial WW domains. Nature (2005) 2.76
Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity. Biochemistry (2004) 2.69
Estimation of the available free energy in a LOV2-J alpha photoswitch. Nat Chem Biol (2008) 2.63
A global analysis of cross-talk in a mammalian cellular signalling network. Nat Cell Biol (2006) 2.39
Dynamic scaffolding in a G protein-coupled signaling system. Cell (2007) 2.22
Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15
The spatial architecture of protein function and adaptation. Nature (2012) 2.14
Structural basis for PAS domain heterodimerization in the basic helix--loop--helix-PAS transcription factor hypoxia-inducible factor. Proc Natl Acad Sci U S A (2003) 2.09
Structure and interactions of PAS kinase N-terminal PAS domain: model for intramolecular kinase regulation. Structure (2002) 2.04
Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor. Proc Natl Acad Sci U S A (2009) 2.02
Allosteric determinants in guanine nucleotide-binding proteins. Proc Natl Acad Sci U S A (2003) 1.91
Hot spots for allosteric regulation on protein surfaces. Cell (2011) 1.89
The third conformation of p38α MAP kinase observed in phosphorylated p38α and in solution. Structure (2010) 1.88
PAS domain-mediated WC-1/WC-2 interaction is essential for maintaining the steady-state level of WC-1 and the function of both proteins in circadian clock and light responses of Neurospora. Mol Cell Biol (2002) 1.82
Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization. J Mol Biol (2005) 1.80
Identification of small-molecule antagonists that inhibit an activator: coactivator interaction. Proc Natl Acad Sci U S A (2004) 1.77
Rationally improving LOV domain-based photoswitches. Nat Methods (2010) 1.72
Allosteric inhibition of hypoxia inducible factor-2 with small molecules. Nat Chem Biol (2013) 1.55
Structure of a bacterial BLUF photoreceptor: insights into blue light-mediated signal transduction. Proc Natl Acad Sci U S A (2005) 1.43
Changes at the KinA PAS-A dimerization interface influence histidine kinase function. Biochemistry (2008) 1.43
An interdomain sector mediating allostery in Hsp70 molecular chaperones. Mol Syst Biol (2010) 1.42
Regulation of C-type lectin antimicrobial activity by a flexible N-terminal prosegment. J Biol Chem (2008) 1.35
Conformational changes in a photosensory LOV domain monitored by time-resolved NMR spectroscopy. J Am Chem Soc (2004) 1.34
Molecular basis for peptidoglycan recognition by a bactericidal lectin. Proc Natl Acad Sci U S A (2010) 1.34
Signal transduction pathway of TonB-dependent transporters. Proc Natl Acad Sci U S A (2006) 1.32
Tripping the light fantastic: blue-light photoreceptors as examples of environmentally modulated protein-protein interactions. Biochemistry (2010) 1.32
A conserved glutamine plays a central role in LOV domain signal transmission and its duration. Biochemistry (2008) 1.23
Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein. Proc Natl Acad Sci U S A (2011) 1.21
Functions of the Per/ARNT/Sim domains of the hypoxia-inducible factor. J Biol Chem (2005) 1.19
Changes in fractal dimension during aggregation. Water Res (2003) 1.17
Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B. J Am Chem Soc (2009) 1.17
Coactivators necessary for transcriptional output of the hypoxia inducible factor, HIF, are directly recruited by ARNT PAS-B. Proc Natl Acad Sci U S A (2011) 1.15
Knowledge-based potentials in protein design. Curr Opin Struct Biol (2006) 1.11
Identification and biosynthesis of cyclic enterobacterial common antigen in Escherichia coli. J Bacteriol (2003) 1.11
Coactivator recruitment: a new role for PAS domains in transcriptional regulation by the bHLH-PAS family. J Cell Physiol (2010) 1.11
Risk factors for preterm, low birth weight and small for gestational age birth in urban Aboriginal and Torres Strait Islander women in Townsville. Aust N Z J Public Health (2006) 1.09
Regulation of nuclear import/export of carbohydrate response element-binding protein (ChREBP): interaction of an alpha-helix of ChREBP with the 14-3-3 proteins and regulation by phosphorylation. J Biol Chem (2008) 1.09
Molecular basis of coiled coil coactivator recruitment by the aryl hydrocarbon receptor nuclear translocator (ARNT). J Biol Chem (2009) 1.05
Mechanism of substrate specificity in Bacillus subtilis ResA, a thioredoxin-like protein involved in cytochrome c maturation. Proc Natl Acad Sci U S A (2006) 1.00
Knowledge-based potential functions in protein design. Curr Opin Struct Biol (2002) 0.99
Local complexity of amino acid interactions in a protein core. Proc Natl Acad Sci U S A (2003) 0.99
Development of inhibitors of the PAS-B domain of the HIF-2α transcription factor. J Med Chem (2013) 0.99
The effects of hydrocephalus on intelligence quotient in children with localized infratentorial ependymoma before and after focal radiation therapy. J Neurosurg (2004) 0.98
ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space. Proc Natl Acad Sci U S A (2009) 0.98
Structure and insight into blue light-induced changes in the BlrP1 BLUF domain. Biochemistry (2009) 0.98
Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Photochem Photobiol Sci (2013) 0.98
Elevated basal slippage mutation rates among the Canidae. J Hered (2007) 0.97
Systems analysis of the single photon response in invertebrate photoreceptors. Proc Natl Acad Sci U S A (2008) 0.97
Identification and optimization of protein domains for NMR studies. Methods Enzymol (2005) 0.96
Structural requirements for key residues and auxiliary portions of a BLUF domain. Biochemistry (2008) 0.96
Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site. Biochemistry (2011) 0.91
Blue light regulated two-component systems: enzymatic and functional analyses of light-oxygen-voltage (LOV)-histidine kinases and downstream response regulators. Biochemistry (2013) 0.91
The erythropoietin receptor transmembrane domain mediates complex formation with viral anemic and polycythemic gp55 proteins. J Biol Chem (2003) 0.91
Identification of natural and artificial DNA substrates for light-activated LOV-HTH transcription factor EL222. Biochemistry (2012) 0.90
Autophagy: Snapshot of the network. Nature (2010) 0.90
Hypoxia-inducible factors Per/ARNT/Sim domains: structure and function. Methods Enzymol (2007) 0.89
Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay. Biochemistry (2011) 0.88
Enlightening molecular mechanisms through study of protein interactions. J Mol Cell Biol (2012) 0.88
Regulating the ARNT/TACC3 axis: multiple approaches to manipulating protein/protein interactions with small molecules. ACS Chem Biol (2012) 0.88
Blue light-induced dimerization of a bacterial LOV-HTH DNA-binding protein. Biochemistry (2013) 0.87
Hemerythrin-like domain within F-box and leucine-rich repeat protein 5 (FBXL5) communicates cellular iron and oxygen availability by distinct mechanisms. J Biol Chem (2012) 0.87
Slow transition between two beta-strand registers is dictated by protein unfolding. J Am Chem Soc (2009) 0.87
Comparative life cycle assessment (LCA) of construction and demolition (C&D) derived biomass and U.S. northeast forest residuals gasification for electricity production. Environ Sci Technol (2013) 0.86
Cyclic enterobacterial common antigen: potential contaminant of bacterially expressed protein preparations. J Biomol NMR (2004) 0.86
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Impacts of natural weathering on the transformation/neoformation processes in landfilled MSWI bottom ash: a geoenvironmental perspective. Waste Manag (2011) 0.85
Evaluation of nitroalkenes as nitric oxide donors. Bioorg Med Chem Lett (2007) 0.84
Evolution-based design of proteins. Methods Enzymol (2013) 0.83
A LOVely view of blue light photosensing. Nat Chem Biol (2007) 0.83
Prognostic factors in patients with node-negative gastric cancer: an Indian experience. World J Surg Oncol (2011) 0.83
Mutational and structural studies of the PixD BLUF output signal that affects light-regulated interactions with PixE. Biochemistry (2011) 0.83
O acetylation of the enterobacterial common antigen polysaccharide is catalyzed by the product of the yiaH gene of Escherichia coli K-12. J Bacteriol (2006) 0.82
Uptake of polycyclic aromatic hydrocarbons (PAHs) in salt marsh plants Spartina alterniflora grown in contaminated sediments. Chemosphere (2005) 0.82
Quantifying the rhythm of KaiB-C interaction for in vitro cyanobacterial circadian clock. PLoS One (2012) 0.81
Preferential binding of K+ ions in the selectivity filter at equilibrium explains high selectivity of K+ channels. J Gen Physiol (2012) 0.80
Dechlorination of polychlorinated biphenyls, naphthalenes and dibenzo-p-dioxins by magnesium/palladium bimetallic particles. J Environ Sci Health A Tox Hazard Subst Environ Eng (2007) 0.80
Ligand-induced folding of a two-component signaling receiver domain. Biochemistry (2015) 0.79
Cosolvent-induced transformation of a death domain tertiary structure. Proc Natl Acad Sci U S A (2002) 0.77
The three Rs of transcription: recruit, retain, and recycle. Mol Cell (2010) 0.77
Methyl labeling and TROSY NMR spectroscopy of proteins expressed in the eukaryote Pichia pastoris. J Biomol NMR (2015) 0.77
Solution structure of the WNK1 autoinhibitory domain, a WNK-specific PF2 domain. J Mol Biol (2013) 0.76
Backyard Pool Party: Not Your Typical Sunburn. Pediatr Emerg Care (2017) 0.75
Special issue as a tribute to Lewis E Kay on his 50th birthday. J Biomol NMR (2011) 0.75
Long-term performance of aged waste forms treated by stabilization/solidification. J Hazard Mater (2010) 0.75
Modeling hydrology and reactive transport in roads: the effect of cracks, the edge, and contaminant properties. Waste Manag (2007) 0.75
Mechanisms for the aging-induced reduction of lead solubility in scrubber residues from municipal solid waste combustion. Waste Manag Res (2002) 0.75
Simultaneous application of dissolution/precipitation and surface complexation/surface precipitation modeling to contaminant leaching. Environ Sci Technol (2005) 0.75
Quality of life of older African American women in rural North Carolina. J Women Aging (2003) 0.75