Published in Proc Natl Acad Sci U S A on December 17, 2009
Protein 3D structure computed from evolutionary sequence variation. PLoS One (2011) 4.71
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Emerging methods in protein co-evolution. Nat Rev Genet (2013) 2.72
Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife (2014) 2.23
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res (2010) 1.95
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci U S A (2012) 1.57
Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. Bioinformatics (2014) 1.17
Interaction fidelity in two-component signaling. Curr Opin Microbiol (2010) 1.15
PconsFold: improved contact predictions improve protein models. Bioinformatics (2014) 1.12
The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. J Phys Chem B (2012) 1.10
Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface (2014) 1.08
Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1. Mol Biol Evol (2015) 1.05
Excited states of ribosome translocation revealed through integrative molecular modeling. Proc Natl Acad Sci U S A (2011) 1.04
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
Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci U S A (2014) 1.03
Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape. J Biol Chem (2010) 1.02
Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1. Proc Natl Acad Sci U S A (2014) 0.98
Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners. PLoS One (2014) 0.97
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev (2016) 0.92
From residue coevolution to protein conformational ensembles and functional dynamics. Proc Natl Acad Sci U S A (2015) 0.92
Molecular Mechanisms of Two-Component Signal Transduction. J Mol Biol (2016) 0.87
Dimeric interactions and complex formation using direct coevolutionary couplings. Sci Rep (2015) 0.86
Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon. PLoS One (2016) 0.85
Statistical analyses of protein sequence alignments identify structures and mechanisms in signal activation of sensor histidine kinases. Mol Microbiol (2012) 0.84
Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. Proc Natl Acad Sci U S A (2016) 0.82
Constructing sequence-dependent protein models using coevolutionary information. Protein Sci (2015) 0.82
Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000Res (2016) 0.80
Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. Nucleic Acids Res (2015) 0.79
Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction. PLoS Comput Biol (2015) 0.79
A three-dimensional topology of complex I inferred from evolutionary correlations. BMC Struct Biol (2012) 0.78
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. Proc Natl Acad Sci U S A (2016) 0.77
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. Mol Biol Evol (2016) 0.76
Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. Proc Natl Acad Sci U S A (2016) 0.76
Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis. Proc Natl Acad Sci U S A (2017) 0.75
Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinformatics (2015) 0.75
A tale of two machines: a review of the BLAST meeting, Tucson, AZ, 20-24 January 2013. Mol Microbiol (2013) 0.75
Native structure-based modeling and simulation of biomolecular systems per mouse click. BMC Bioinformatics (2014) 0.75
Evolutionary pressure on the topology of protein interface interaction networks. J Phys Chem B (2013) 0.75
Investigating co-evolution of functionally associated phosphosites in human. Mol Genet Genomics (2014) 0.75
RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res (2001) 45.29
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
GROMACS: fast, flexible, and free. J Comput Chem (2005) 27.22
The energy landscapes and motions of proteins. Science (1991) 18.93
Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins (1995) 14.36
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc (2003) 11.65
Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature (2007) 9.12
Theory of protein folding. Curr Opin Struct Biol (2004) 7.64
Protein structure modeling with MODELLER. Methods Mol Biol (2008) 6.28
Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem Sci (2001) 6.27
Two-component and phosphorelay signal transduction. Curr Opin Microbiol (2000) 5.70
Rewiring the specificity of two-component signal transduction systems. Cell (2008) 4.80
Biological insights from structures of two-component proteins. Annu Rev Microbiol (2009) 4.47
Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A (2008) 4.37
Are current molecular dynamics force fields too helical? Biophys J (2008) 3.13
Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction. Cell (2009) 2.94
Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J (2005) 2.85
A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Structure (2000) 2.71
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44
Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol (2008) 2.09
Molecular recognition in signal transduction: the interaction surfaces of the Spo0F response regulator with its cognate phosphorelay proteins revealed by alanine scanning mutagenesis. J Mol Biol (1997) 1.86
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J Mol Biol (2001) 1.86
Sensor complexes regulating two-component signal transduction. Curr Opin Struct Biol (2007) 1.82
Keeping signals straight in phosphorelay signal transduction. J Bacteriol (2001) 1.72
Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods Enzymol (2007) 1.54
Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase. Mol Cell (1998) 1.51
Optimizing physical energy functions for protein folding. Proteins (2004) 1.49
Robustness and generalization of structure-based models for protein folding and function. Proteins (2009) 1.29
The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface. J Bacteriol (2003) 1.27
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state. J Bacteriol (2006) 1.24
Speeding up parallel GROMACS on high-latency networks. J Comput Chem (2007) 1.23
Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G. J Am Chem Soc (2003) 1.23
Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proc Natl Acad Sci U S A (2007) 1.20
Reproducible protein folding with the stochastic tunneling method. Phys Rev Lett (2003) 1.12
Co-evolving motions at protein-protein interfaces of two-component signaling systems identified by covariance analysis. Biochemistry (2008) 1.06
Metals in the sporulation phosphorelay: manganese binding by the response regulator Spo0F. Acta Crystallogr D Biol Crystallogr (2004) 0.98
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models. J Phys Chem B (2008) 0.93
Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition. FEBS Lett (2007) 0.85
A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophys J (2004) 0.84
Identification of a novel two component system in Thermotoga maritima. Complex stoichiometry and crystallization. Biochim Biophys Acta (2007) 0.78
On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A (2003) 6.02
Transcriptional regulation by the numbers: models. Curr Opin Genet Dev (2005) 5.20
Interdependence of cell growth and gene expression: origins and consequences. Science (2010) 5.00
Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A (2008) 4.37
Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A (2011) 4.08
Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci U S A (2002) 3.78
Growth rate-dependent global effects on gene expression in bacteria. Cell (2009) 3.57
Transcriptional regulation by the numbers: applications. Curr Opin Genet Dev (2005) 3.40
Quantitative characteristics of gene regulation by small RNA. PLoS Biol (2007) 3.35
Water mediation in protein folding and molecular recognition. Annu Rev Biophys Biomol Struct (2006) 3.32
Protein topology determines binding mechanism. Proc Natl Acad Sci U S A (2003) 3.16
Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A (2002) 3.07
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature (2010) 2.85
Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc Natl Acad Sci U S A (2003) 2.80
Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc Natl Acad Sci U S A (2007) 2.51
Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol (2006) 2.49
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44
Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. Phys Rev E Stat Nonlin Soft Matter Phys (2013) 2.31
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol (2005) 1.99
Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. J Am Chem Soc (2004) 1.99
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res (2010) 1.95
Domain swapping is a consequence of minimal frustration. Proc Natl Acad Sci U S A (2004) 1.93
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA (2010) 1.91
Absolute rate theories of epigenetic stability. Proc Natl Acad Sci U S A (2005) 1.89
Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci U S A (2008) 1.87
Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. J Am Chem Soc (2007) 1.85
Topological frustration and the folding of interleukin-1 beta. J Mol Biol (2005) 1.77
DNA sequence evolution with neighbor-dependent mutation. J Comput Biol (2003) 1.76
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. J Mol Biol (2003) 1.74
Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol (2003) 1.72
Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature (2013) 1.70
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc Natl Acad Sci U S A (2009) 1.65
Nonlinear protein degradation and the function of genetic circuits. Proc Natl Acad Sci U S A (2005) 1.65
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination. Proc Natl Acad Sci U S A (2013) 1.60
Simple energy landscape model for the kinetics of functional transitions in proteins. J Phys Chem B (2005) 1.57
Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis. Proc Natl Acad Sci U S A (2012) 1.57
On the selection and evolution of regulatory DNA motifs. J Mol Evol (2002) 1.55
Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics (2005) 1.54
Mechanical control of the directional stepping dynamics of the kinesin motor. Proc Natl Acad Sci U S A (2007) 1.54
Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods Enzymol (2007) 1.54
Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc Natl Acad Sci U S A (2007) 1.54
Bacterial growth laws and their applications. Curr Opin Biotechnol (2011) 1.52
Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophys J (2009) 1.51
Internal strain regulates the nucleotide binding site of the kinesin leading head. Proc Natl Acad Sci U S A (2007) 1.50
Understanding protein folding with energy landscape theory. Part I: Basic concepts. Q Rev Biophys (2002) 1.49
Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects. J Mol Evol (2005) 1.45
Small RNAs establish gene expression thresholds. Curr Opin Microbiol (2008) 1.44
Sequential establishment of stripe patterns in an expanding cell population. Science (2011) 1.44
A Stevedore's protein knot. PLoS Comput Biol (2010) 1.43
Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc Natl Acad Sci U S A (2005) 1.42
Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci U S A (2008) 1.41
Stochastic fluctuations in metabolic pathways. Proc Natl Acad Sci U S A (2007) 1.39
Understanding stochastic simulations of the smallest genetic networks. J Chem Phys (2007) 1.37
Understanding protein folding with energy landscape theory. Part II: Quantitative aspects. Q Rev Biophys (2002) 1.35
Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: tunneling across an aqueous interface. Proc Natl Acad Sci U S A (2005) 1.35
Extracting function from a beta-trefoil folding motif. Proc Natl Acad Sci U S A (2008) 1.34
The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science (2013) 1.34
Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein. Proc Natl Acad Sci U S A (2011) 1.31
Mechanisms of protein assembly: lessons from minimalist models. Acc Chem Res (2006) 1.30
Robustness and generalization of structure-based models for protein folding and function. Proteins (2009) 1.29
On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient. Proc Natl Acad Sci U S A (2012) 1.28
Conformational transitions in adenylate kinase. Allosteric communication reduces misligation. J Biol Chem (2007) 1.27
Multiple routes lead to the native state in the energy landscape of the beta-trefoil family. Proc Natl Acad Sci U S A (2006) 1.25
Ligand-induced global transitions in the catalytic domain of protein kinase A. Proc Natl Acad Sci U S A (2009) 1.25
Sources and sinks: a stochastic model of evolution in heterogeneous environments. Phys Rev Lett (2010) 1.24
Mechanically probing the folding pathway of single RNA molecules. Biophys J (2003) 1.23
A sensor histidine kinase co-ordinates cell wall architecture with cell division in Bacillus subtilis. Mol Microbiol (2008) 1.23
Backtracking on the folding landscape of the beta-trefoil protein interleukin-1beta? Proc Natl Acad Sci U S A (2008) 1.22
Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proc Natl Acad Sci U S A (2007) 1.20
Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS One (2011) 1.20
Molecular crowding limits translation and cell growth. Proc Natl Acad Sci U S A (2013) 1.19
The dual-basin landscape in GFP folding. Proc Natl Acad Sci U S A (2008) 1.16
Phosphorylation and functional analysis of the sporulation initiation factor Spo0A from Clostridium botulinum. Mol Microbiol (2006) 1.15
Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A (2010) 1.15
Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center. Proc Natl Acad Sci U S A (2004) 1.15
Deterministic characterization of stochastic genetic circuits. Proc Natl Acad Sci U S A (2007) 1.15
NAF-1 and mitoNEET are central to human breast cancer proliferation by maintaining mitochondrial homeostasis and promoting tumor growth. Proc Natl Acad Sci U S A (2013) 1.14
Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc Natl Acad Sci U S A (2013) 1.14
A driving and coupling "Pac-Man" mechanism for chromosome poleward translocation in anaphase A. Proc Natl Acad Sci U S A (2006) 1.13
Biomolecular dynamics: order-disorder transitions and energy landscapes. Rep Prog Phys (2012) 1.12
Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci U S A (2011) 1.11
The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. J Phys Chem B (2012) 1.10
Need-based activation of ammonium uptake in Escherichia coli. Mol Syst Biol (2012) 1.10
Folding time predictions from all-atom replica exchange simulations. J Mol Biol (2007) 1.09
Regional and time-resolved mutation patterns of the human genome. Bioinformatics (2004) 1.08
Hybrid alignment: high-performance with universal statistics. Bioinformatics (2002) 1.07
Direct single-molecule observation of a protein living in two opposed native structures. Proc Natl Acad Sci U S A (2009) 1.07
Designing sequential transcription logic: a simple genetic circuit for conditional memory. Syst Synth Biol (2007) 1.07