Published in Proteins on March 01, 2006
The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol (2009) 6.58
Ion channel voltage sensors: structure, function, and pathophysiology. Neuron (2010) 3.16
Three-dimensional structures of membrane proteins from genomic sequencing. Cell (2012) 3.02
Structure of the chemokine receptor CXCR1 in phospholipid bilayers. Nature (2012) 2.88
Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci U S A (2006) 2.81
Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J (2008) 2.53
Toward high-resolution prediction and design of transmembrane helical protein structures. Proc Natl Acad Sci U S A (2007) 2.12
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (2011) 2.11
Sequential formation of ion pairs during activation of a sodium channel voltage sensor. Proc Natl Acad Sci U S A (2009) 1.79
Prediction of membrane protein structures with complex topologies using limited constraints. Proc Natl Acad Sci U S A (2009) 1.73
Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy. Structure (2011) 1.68
Structural basis for gating charge movement in the voltage sensor of a sodium channel. Proc Natl Acad Sci U S A (2011) 1.68
Structure and function of the voltage sensor of sodium channels probed by a beta-scorpion toxin. J Biol Chem (2006) 1.58
Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. Prog Nucl Magn Reson Spectrosc (2009) 1.57
RosettaEPR: an integrated tool for protein structure determination from sparse EPR data. J Struct Biol (2010) 1.50
Gating charge interactions with the S1 segment during activation of a Na+ channel voltage sensor. Proc Natl Acad Sci U S A (2011) 1.40
Structural models for the KCNQ1 voltage-gated potassium channel. Biochemistry (2007) 1.38
Structure determination of a membrane protein in proteoliposomes. J Am Chem Soc (2012) 1.37
Mapping the receptor site for alpha-scorpion toxins on a Na+ channel voltage sensor. Proc Natl Acad Sci U S A (2011) 1.36
Selective disruption of high sensitivity heat activation but not capsaicin activation of TRPV1 channels by pore turret mutations. J Gen Physiol (2012) 1.21
Prediction of transmembrane helix orientation in polytopic membrane proteins. BMC Struct Biol (2006) 1.19
Identification of residues defining phospholipid flippase substrate specificity of type IV P-type ATPases. Proc Natl Acad Sci U S A (2012) 1.18
MEDELLER: homology-based coordinate generation for membrane proteins. Bioinformatics (2010) 1.12
Structural mechanism underlying capsaicin binding and activation of the TRPV1 ion channel. Nat Chem Biol (2015) 1.11
MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes. Structure (2015) 1.08
Structure-function map of the receptor site for β-scorpion toxins in domain II of voltage-gated sodium channels. J Biol Chem (2011) 1.05
Probing the metabotropic glutamate receptor 5 (mGlu₅) positive allosteric modulator (PAM) binding pocket: discovery of point mutations that engender a "molecular switch" in PAM pharmacology. Mol Pharmacol (2013) 1.05
Reconstruction of protein backbones from the BriX collection of canonical protein fragments. PLoS Comput Biol (2008) 1.04
PGY repeats and N-glycans govern the trafficking of paranodin and its selective association with contactin and neurofascin-155. Mol Biol Cell (2006) 1.03
Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination. J Struct Biol (2010) 1.02
Mapping the interaction site for a β-scorpion toxin in the pore module of domain III of voltage-gated Na(+) channels. J Biol Chem (2012) 0.99
Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc (2013) 0.96
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. Bioinformatics (2013) 0.95
An ab Initio structural model of a nucleoside permease predicts functionally important residues. J Biol Chem (2009) 0.95
Chemoselective tarantula toxins report voltage activation of wild-type ion channels in live cells. Proc Natl Acad Sci U S A (2014) 0.94
Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy. Annu Rev Anal Chem (Palo Alto Calif) (2013) 0.93
Interactions of H562 in the S5 helix with T618 and S621 in the pore helix are important determinants of hERG1 potassium channel structure and function. Biophys J (2009) 0.92
Characterization and modeling of the oligomeric state and ligand binding behavior of purified translocator protein 18 kDa from Rhodobacter sphaeroides. Biochemistry (2013) 0.92
A unified hydrophobicity scale for multispan membrane proteins. Proteins (2009) 0.92
Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins (2010) 0.92
Structure determination of membrane proteins in five easy pieces. Methods (2011) 0.91
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin. Elife (2016) 0.90
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra. J Magn Reson (2011) 0.90
Predictive energy landscapes for folding α-helical transmembrane proteins. Proc Natl Acad Sci U S A (2014) 0.89
Both sequence and context are important for flagellar targeting of a glucose transporter. J Cell Sci (2012) 0.88
Computational studies of membrane proteins: models and predictions for biological understanding. Biochim Biophys Acta (2011) 0.88
Characterizing and predicting the functional and conformational diversity of seven-transmembrane proteins. Methods (2011) 0.87
BCL::MP-fold: folding membrane proteins through assembly of transmembrane helices. Structure (2013) 0.87
End-point targeted molecular dynamics: large-scale conformational changes in potassium channels. Biophys J (2008) 0.87
Computational and functional analyses of a small-molecule binding site in ROMK. Biophys J (2015) 0.87
Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys J (2007) 0.86
BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints. Proteins (2015) 0.86
Catalytic residues and a predicted structure of tetrahydrobiopterin-dependent alkylglycerol mono-oxygenase. Biochem J (2012) 0.85
Identification of determinants required for agonistic and inverse agonistic ligand properties at the ADP receptor P2Y12. Mol Pharmacol (2012) 0.85
An Integrated Framework Advancing Membrane Protein Modeling and Design. PLoS Comput Biol (2015) 0.84
Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. BMC Bioinformatics (2008) 0.84
TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. BMC Bioinformatics (2015) 0.84
Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors. PLoS One (2013) 0.84
A patient with posterior cortical atrophy possesses a novel mutation in the presenilin 1 gene. PLoS One (2013) 0.84
Na⁺/K⁺-ATPase E960 and phospholemman F28 are critical for their functional interaction. Proc Natl Acad Sci U S A (2012) 0.84
Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS One (2013) 0.84
Computational modeling of membrane proteins. Proteins (2014) 0.83
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PLoS Comput Biol (2016) 0.83
Transmembrane protein alignment and fold recognition based on predicted topology. PLoS One (2013) 0.83
Modulation of constitutive activity and signaling bias of the ghrelin receptor by conformational constraint in the second extracellular loop. J Biol Chem (2012) 0.83
EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib. BMC Bioinformatics (2015) 0.83
Improved chemical shift prediction by Rosetta conformational sampling. J Biomol NMR (2012) 0.82
Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane. Elife (2016) 0.81
Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors. Expert Opin Drug Discov (2008) 0.81
Membrane protein native state discrimination by implicit membrane models. J Comput Chem (2012) 0.81
RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils. Nucleic Acids Res (2009) 0.81
Unique interaction pattern for a functionally biased ghrelin receptor agonist. J Biol Chem (2011) 0.81
Membrane protein orientation and refinement using a knowledge-based statistical potential. BMC Bioinformatics (2013) 0.80
Canonical azimuthal rotations and flanking residues constrain the orientation of transmembrane helices. Biophys J (2013) 0.80
Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. J Comput Aided Mol Des (2012) 0.79
Interactions between ionizable amino acid side chains at a lipid bilayer-water interface. J Phys Chem B (2011) 0.79
The Aspergillus nidulans proline permease as a model for understanding the factors determining substrate binding and specificity of fungal amino acid transporters. J Biol Chem (2015) 0.79
A Polybasic Plasma Membrane Binding Motif in the I-II Linker Stabilizes Voltage-gated CaV1.2 Calcium Channel Function. J Biol Chem (2015) 0.79
Assembly and Stability of α-Helical Membrane Proteins. Soft Matter (2012) 0.79
Pancreatic polypeptide is recognized by two hydrophobic domains of the human Y4 receptor binding pocket. J Biol Chem (2013) 0.78
Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch. Sci Rep (2015) 0.78
Computational and genetic evidence that different structural conformations of a non-catalytic region affect the function of plant cellulose synthase. J Exp Bot (2014) 0.78
Activity-Dependent Palmitoylation Controls SynDIG1 Stability, Localization, and Function. J Neurosci (2016) 0.78
A pain-inducing centipede toxin targets the heat activation machinery of nociceptor TRPV1. Nat Commun (2015) 0.78
Rational design and validation of a vanilloid-sensitive TRPV2 ion channel. Proc Natl Acad Sci U S A (2016) 0.78
Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling. J Gen Physiol (2016) 0.77
The homology model of PMP22 suggests mutations resulting in peripheral neuropathy disrupt transmembrane helix packing. Biochemistry (2014) 0.77
Structure of the membrane protein MerF, a bacterial mercury transporter, improved by the inclusion of chemical shift anisotropy constraints. J Biomol NMR (2014) 0.77
Probabilistic grammatical model for helix-helix contact site classification. Algorithms Mol Biol (2013) 0.77
Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. Acta Crystallogr D Biol Crystallogr (2013) 0.77
Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci (2016) 0.77
Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology. Proc Natl Acad Sci U S A (2016) 0.76
Mechanisms of Calmodulin Regulation of Different Isoforms of Kv7.4 K+ Channels. J Biol Chem (2015) 0.76
Toward high-resolution computational design of the structure and function of helical membrane proteins. Nat Struct Mol Biol (2016) 0.76
A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site. PLoS One (2016) 0.76
Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin. PLoS One (2015) 0.76
Finding Channels. J Biol Chem (2015) 0.76
Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor. J Comput Aided Mol Des (2013) 0.76
Membrane protein structure from rotational diffusion. Biochim Biophys Acta (2014) 0.76
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Crystal structure of rhodopsin: A G protein-coupled receptor. Science (2000) 28.60
Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29
The PSIPRED protein structure prediction server. Bioinformatics (2000) 20.58
A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol (1998) 14.18
The druggable genome. Nat Rev Drug Discov (2002) 13.61
The HMMTOP transmembrane topology prediction server. Bioinformatics (2001) 12.57
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol (1997) 10.38
Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct (1999) 10.13
LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res (2003) 9.44
X-ray structure of a protein-conducting channel. Nature (2003) 9.20
Toward high-resolution de novo structure prediction for small proteins. Science (2005) 9.18
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci (1998) 7.88
Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol (1998) 7.72
A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry (1994) 6.64
The preference of tryptophan for membrane interfaces. Biochemistry (1998) 5.10
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins (1999) 4.86
X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science (1997) 4.74
Helical membrane protein folding, stability, and evolution. Annu Rev Biochem (2000) 3.63
Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol (2000) 3.12
Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol (2000) 2.97
De novo prediction of three-dimensional structures for major protein families. J Mol Biol (2002) 2.88
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
Hydrophobic organization of membrane proteins. Science (1989) 2.74
Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics (2004) 2.70
An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol (1997) 2.66
Predicting novel protein folds by using FRAGFOLD. Proteins (2001) 2.65
Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci U S A (2001) 2.64
Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J (1999) 2.49
Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci U S A (2001) 2.47
The functions of tryptophan residues in membrane proteins. Protein Eng (1992) 2.45
Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta (2001) 2.43
Do transmembrane protein superfolds exist? FEBS Lett (1998) 2.40
Comparing function and structure between entire proteomes. Protein Sci (2001) 2.18
Internal packing of helical membrane proteins. Proc Natl Acad Sci U S A (2000) 2.12
Free modeling with Rosetta in CASP6. Proteins (2005) 2.10
What is the value added by human intervention in protein structure prediction? Proteins (2001) 1.97
Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys J (2002) 1.88
Properties of integral membrane protein structures: derivation of an implicit membrane potential. Proteins (2005) 1.74
A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat Struct Biol (1999) 1.68
Topogenesis of membrane proteins at the endoplasmic reticulum. Biochemistry (2004) 1.59
Helix packing moments reveal diversity and conservation in membrane protein structure. J Mol Biol (2004) 1.53
Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J Mol Biol (2001) 1.50
Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers. Proteins (2002) 1.43
A method for alpha-helical integral membrane protein fold prediction. Proteins (1994) 1.42
Helical packing patterns in membrane and soluble proteins. Biophys J (2004) 1.30
A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices. J Mol Biol (2002) 1.29
An approach to membrane protein structure without crystals. Proc Natl Acad Sci U S A (2002) 1.28
Are there dominant membrane protein families with a given number of helices? Proteins (1997) 1.26
Refolding of bacteriorhodopsin from expressed polypeptide fragments. J Biol Chem (1998) 1.25
A simple method for modeling transmembrane helix oligomers. J Mol Biol (2003) 1.19
Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins (2005) 1.19
PREDICT modeling and in-silico screening for G-protein coupled receptors. Proteins (2004) 1.18
Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins (1997) 1.11
A new method to model membrane protein structure based on silent amino acid substitutions. Proteins (2001) 1.09
Structure. Rhodopsin sees the light. Science (2000) 1.05
kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction. J Mol Biol (1999) 1.04
Modeling the 3D structure of GPCRs from sequence. Med Res Rev (2001) 1.01
Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures. Proteins (2003) 1.00
An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J (2004) 1.00
Side chains in transmembrane helices are shorter at helix-helix interfaces. Proteins (2000) 0.93
Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices. Proteins (2004) 0.88
Optimal potentials for predicting inter-helical packing in transmembrane proteins. Proteins (2002) 0.86
Shorter side chains optimize helix-helix packing. Protein Sci (2004) 0.83
Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT. Protein Eng Des Sel (2005) 0.79
Design of a novel globular protein fold with atomic-level accuracy. Science (2003) 13.06
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
Predicting protein structures with a multiplayer online game. Nature (2010) 9.95
Toward high-resolution de novo structure prediction for small proteins. Science (2005) 9.18
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol (2003) 8.35
Macromolecular modeling with rosetta. Annu Rev Biochem (2008) 8.32
Kemp elimination catalysts by computational enzyme design. Nature (2008) 8.19
Evaluation of structural and evolutionary contributions to deleterious mutation prediction. J Mol Biol (2002) 7.79
High-resolution structure prediction and the crystallographic phase problem. Nature (2007) 7.67
De novo computational design of retro-aldol enzymes. Science (2008) 7.62
Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res (2004) 7.39
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33
Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A (2008) 6.76
A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci U S A (2002) 6.18
Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nat Struct Mol Biol (2011) 5.02
Towards robust regional estimates of CO2 sources and sinks using atmospheric transport models. Nature (2002) 4.71
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol (2003) 4.63
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chem Biol (2006) 4.52
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science (2011) 4.42
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science (2010) 4.32
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins (2009) 4.27
Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006) 4.06
Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature (2010) 4.04
Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A (2007) 3.87
Algorithm discovery by protein folding game players. Proc Natl Acad Sci U S A (2011) 3.74
Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol (2004) 3.66
Modeling structurally variable regions in homologous proteins with rosetta. Proteins (2004) 3.64
Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins (2009) 3.64
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins (2006) 3.60
Rational HIV immunogen design to target specific germline B cell receptors. Science (2013) 3.55
High-resolution mapping of protein sequence-function relationships. Nat Methods (2010) 3.47
Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature (2006) 3.45
Computational alanine scanning of protein-protein interfaces. Sci STKE (2004) 3.41
Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003) 3.41
New algorithms and an in silico benchmark for computational enzyme design. Protein Sci (2006) 3.40
Simplification of antiretroviral therapy with tenofovir-emtricitabine or abacavir-Lamivudine: a randomized, 96-week trial. Clin Infect Dis (2009) 3.32
Inflammation in neurodegenerative diseases. Immunology (2010) 3.22
An engineered microbial platform for direct biofuel production from brown macroalgae. Science (2012) 3.20
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol (2003) 3.08
Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods (2010) 3.07
Progress in modeling of protein structures and interactions. Science (2005) 3.05
Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci U S A (2009) 3.01
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007) 3.01
NMR structure determination for larger proteins using backbone-only data. Science (2010) 3.00
Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol (2009) 2.94
The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci U S A (2006) 2.88
De novo prediction of three-dimensional structures for major protein families. J Mol Biol (2002) 2.88
RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol (2008) 2.86
Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci U S A (2006) 2.81
Computational thermostabilization of an enzyme. Science (2005) 2.79
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
Improved molecular replacement by density- and energy-guided protein structure optimization. Nature (2011) 2.74
Improved side-chain modeling for protein-protein docking. Protein Sci (2005) 2.72
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A (2004) 2.71
Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A (2010) 2.68
Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins (2010) 2.56
CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods (2009) 2.50
A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell (2007) 2.50
Principles for designing ideal protein structures. Nature (2012) 2.50
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature (2011) 2.49
Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci U S A (2006) 2.47
Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature (2011) 2.46
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR (2008) 2.43
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci U S A (2013) 2.43
No effect of rosiglitazone for treatment of HIV-1 lipoatrophy: randomised, double-blind, placebo-controlled trial. Lancet (2004) 2.43
Computational design of protein-protein interactions. Curr Opin Chem Biol (2004) 2.39
Contact order revisited: influence of protein size on the folding rate. Protein Sci (2003) 2.37
Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci U S A (2007) 2.35
Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science (2012) 2.33
Progress and challenges in high-resolution refinement of protein structure models. Proteins (2005) 2.28
Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell (2002) 2.25
RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One (2011) 2.21
A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature (2011) 2.20
Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol (2012) 2.19
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (2011) 2.17
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol (2012) 2.14
De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc (2002) 2.12
Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol (2011) 2.12
Free modeling with Rosetta in CASP6. Proteins (2005) 2.10
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins (2006) 2.07
Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc Natl Acad Sci U S A (2011) 2.03
Atomic model of the type III secretion system needle. Nature (2012) 2.02
A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nat Struct Mol Biol (2009) 2.02
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. PLoS Biol (2006) 1.99
High-resolution comparative modeling with RosettaCM. Structure (2013) 1.96
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci (2009) 1.96
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res (2006) 1.96
An improved protein decoy set for testing energy functions for protein structure prediction. Proteins (2003) 1.94
Prediction of CASP6 structures using automated Robetta protocols. Proteins (2005) 1.94
Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J Mol Biol (2006) 1.93
Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure (2010) 1.91
Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol (2010) 1.90
A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol (2004) 1.90
Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci U S A (2003) 1.90