Published in Protein Sci on April 01, 2003
The folding of single domain proteins--have we reached a consensus? Curr Opin Struct Biol (2010) 1.42
Kinetic barriers and the role of topology in protein and RNA folding. Protein Sci (2008) 1.07
Frustration in biomolecules. Q Rev Biophys (2014) 1.05
Quantifying the structural requirements of the folding transition state of protein A and other systems. J Mol Biol (2008) 1.05
Hydration of the folding transition state ensemble of a protein. Biochemistry (2006) 0.93
NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR (1995) 93.94
Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A (2000) 7.99
Chemical shifts as a tool for structure determination. Methods Enzymol (1994) 6.12
Recent evidence for evolution of the genetic code. Microbiol Rev (1992) 4.32
A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. 1991. J Magn Reson (2011) 3.69
Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol (1999) 3.50
Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett (1988) 3.49
The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol (1999) 2.93
De novo design of the hydrophobic cores of proteins. Protein Sci (1995) 2.87
Solution structure of the SH3 domain of Src and identification of its ligand-binding site. Science (1992) 2.56
Protein stability parameters measured by hydrogen exchange. Proteins (1994) 2.55
Functional rapidly folding proteins from simplified amino acid sequences. Nat Struct Biol (1997) 2.08
Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Biochemistry (1997) 1.83
Redesigning the hydrophobic core of a four-helix-bundle protein. Protein Sci (1994) 1.79
What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties. Protein Sci (1996) 1.76
Folding dynamics of the src SH3 domain. Biochemistry (1997) 1.72
A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc Natl Acad Sci U S A (1996) 1.56
Characterization of the three-dimensional solution structure of human profilin: 1H, 13C, and 15N NMR assignments and global folding pattern. Biochemistry (1993) 1.42
Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state. J Mol Biol (2002) 1.28
Structural characterization of folded and unfolded states of an SH3 domain in equilibrium in aqueous buffer. Biochemistry (1995) 1.25
Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. Biochemistry (1991) 1.24
Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR. Protein Sci (1996) 1.23
Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data. J Biomol NMR (1997) 1.22
A designed four helix bundle protein with native-like structure. Nat Struct Biol (1997) 1.17
Characterization of NADP+ binding to perdeuterated MurB: backbone atom NMR assignments and chemical-shift changes. J Mol Biol (1997) 1.00
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
Recognition of antimicrobial peptides by a bacterial sensor kinase. Cell (2005) 4.78
Towards robust regional estimates of CO2 sources and sinks using atmospheric transport models. Nature (2002) 4.71
Mutant adenosine deaminase 2 in a polyarteritis nodosa vasculopathy. N Engl J Med (2014) 4.70
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
E2-BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages. Nat Struct Mol Biol (2007) 3.72
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
UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature (2011) 3.40
Simplification of antiretroviral therapy with tenofovir-emtricitabine or abacavir-Lamivudine: a randomized, 96-week trial. Clin Infect Dis (2009) 3.32
A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination. Mol Cell (2006) 3.30
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
Multipass membrane protein structure prediction using Rosetta. Proteins (2006) 2.79
Computational thermostabilization of an enzyme. Science (2005) 2.79
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. Am J Hum Genet (2010) 2.76
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
No effect of rosiglitazone for treatment of HIV-1 lipoatrophy: randomised, double-blind, placebo-controlled trial. Lancet (2004) 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
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
Mutations in mitochondrial histidyl tRNA synthetase HARS2 cause ovarian dysgenesis and sensorineural hearing loss of Perrault syndrome. Proc Natl Acad Sci U S A (2011) 2.11
Free modeling with Rosetta in CASP6. Proteins (2005) 2.10
Structure of an E3:E2~Ub complex reveals an allosteric mechanism shared among RING/U-box ligases. Mol Cell (2012) 2.07
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
Activation of the bacterial sensor kinase PhoQ by acidic pH. Mol Cell (2007) 1.98
Mass spectrometric and mutational analyses reveal Lys-6-linked polyubiquitin chains catalyzed by BRCA1-BARD1 ubiquitin ligase. J Biol Chem (2003) 1.97
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