Published in Proteins on May 15, 2004
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
Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009) 5.67
Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc (2009) 5.42
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
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA (2009) 2.63
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure (2011) 2.61
Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry (2010) 2.56
Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci U S A (2006) 2.47
Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol (2008) 2.27
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov (2009) 2.23
Function of a conserved checkpoint recruitment domain in ATRIP proteins. Mol Cell Biol (2007) 2.02
Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res (2006) 1.96
Loop modeling: Sampling, filtering, and scoring. Proteins (2008) 1.81
Computer-aided design of functional protein interactions. Nat Chem Biol (2009) 1.73
High-resolution design of a protein loop. Proc Natl Acad Sci U S A (2007) 1.68
RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS One (2011) 1.59
Structure and function of the voltage sensor of sodium channels probed by a beta-scorpion toxin. J Biol Chem (2006) 1.58
Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins (2009) 1.57
Alteration of enzyme specificity by computational loop remodeling and design. Proc Natl Acad Sci U S A (2009) 1.56
A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. J Exp Med (2007) 1.51
Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol (2010) 1.44
Structural models for the KCNQ1 voltage-gated potassium channel. Biochemistry (2007) 1.38
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure (2009) 1.32
Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies. Proteins (2009) 1.32
Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors. Proc Natl Acad Sci U S A (2011) 1.30
RPBS: a web resource for structural bioinformatics. Nucleic Acids Res (2005) 1.28
Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors. Proteins (2010) 1.27
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins (2008) 1.25
Protein loop modeling by using fragment assembly and analytical loop closure. Proteins (2010) 1.25
The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biol (2013) 1.21
A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res (2006) 1.18
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling. Proteins (2011) 1.13
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol (2006) 1.12
Cryo-electron microscopy structure of an adenovirus-integrin complex indicates conformational changes in both penton base and integrin. J Virol (2009) 1.08
Structural dynamics of the magnesium-bound conformation of CorA in a lipid bilayer. Structure (2010) 1.07
Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field. Protein Eng Des Sel (2008) 1.06
Structure-guided forcefield optimization. Proteins (2011) 1.06
Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins (2014) 1.05
Selective 5-hydroxytryptamine 2C receptor agonists derived from the lead compound tranylcypromine: identification of drugs with antidepressant-like action. J Med Chem (2009) 1.04
Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering. Biochemistry (2010) 1.04
Membrane driven spatial organization of GPCRs. Sci Rep (2013) 1.03
The bipolar assembly domain of the mitotic motor kinesin-5. Nat Commun (2013) 1.03
BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements. PLoS One (2012) 1.01
Structure prediction of domain insertion proteins from structures of individual domains. Structure (2008) 1.01
Loopholes and missing links in protein modeling. Protein Sci (2007) 1.01
Saturating representation of loop conformational fragments in structure databanks. BMC Struct Biol (2006) 1.00
BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements. PLoS One (2012) 1.00
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling. J Mol Biol (2007) 1.00
The C. elegans SYS-1 protein is a bona fide beta-catenin. Dev Cell (2008) 0.97
Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking. Proteins (2010) 0.97
A self-organizing algorithm for modeling protein loops. PLoS Comput Biol (2009) 0.96
Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc (2013) 0.96
Anchored design of protein-protein interfaces. PLoS One (2011) 0.96
FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins (2010) 0.95
Ab initio computational modeling of long loops in G-protein coupled receptors. J Comput Aided Mol Des (2006) 0.94
Progress in super long loop prediction. Proteins (2011) 0.94
Circularly permuted monomeric red fluorescent proteins with new termini in the beta-sheet. Protein Sci (2010) 0.93
Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein Sci (2010) 0.92
Mapping early conformational changes in alphaIIb and beta3 during biogenesis reveals a potential mechanism for alphaIIbbeta3 adopting its bent conformation. Blood (2007) 0.92
Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophys J (2014) 0.91
Exploring the universe of protein structures beyond the Protein Data Bank. PLoS Comput Biol (2010) 0.91
Working model for the structural basis for KCNE1 modulation of the KCNQ1 potassium channel. Curr Opin Struct Biol (2011) 0.90
Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC Bioinformatics (2005) 0.89
Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling. J Am Chem Soc (2008) 0.88
Structure prediction of loops with fixed and flexible stems. J Phys Chem B (2012) 0.88
Ab initio protein modeling into CryoEM density maps using EM-Fold. Biopolymers (2012) 0.88
Internal proton transfer in the external pyridoxal 5'-phosphate Schiff base in dopa decarboxylase. Biochemistry (2010) 0.88
An intrinsically disordered region of the adenovirus capsid is implicated in neutralization by human alpha defensin 5. PLoS One (2013) 0.87
Computed structures of point deletion mutants and their enzymatic activities. Proteins (2011) 0.86
Template-based protein structure modeling. Methods Mol Biol (2010) 0.86
Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations. Biophys J (2015) 0.85
Phylogenetic conservation and homology modeling help reveal a novel domain within the budding yeast heterochromatin protein Sir1. Mol Cell Biol (2008) 0.84
Antibodies as a model system for comparative model refinement. Proteins (2010) 0.84
Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications. J Mol Biol (2011) 0.84
In vivo oligomerization of the F conjugative coupling protein TraD. J Bacteriol (2007) 0.83
Unglycosylation at Asn-633 made extracellular domain of E-cadherin folded incorrectly and arrested in endoplasmic reticulum, then sequentially degraded by ERAD. Glycoconj J (2008) 0.83
Conformational sampling in template-free protein loop structure modeling: an overview. Comput Struct Biotechnol J (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
Octarellin VI: using rosetta to design a putative artificial (β/α)8 protein. PLoS One (2013) 0.82
Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling. PLoS One (2013) 0.82
Improving the accuracy of template-based predictions by mixing and matching between initial models. BMC Struct Biol (2008) 0.82
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PLoS One (2015) 0.82
Analysis of loop boundaries using different local structure assignment methods. Protein Sci (2009) 0.82
SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations. Proteins (2011) 0.82
ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction. AIChE J (2011) 0.82
Near-native protein loop sampling using nonparametric density estimation accommodating sparcity. PLoS Comput Biol (2011) 0.82
A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. J Comput Biol (2011) 0.82
Improving predicted protein loop structure ranking using a Pareto-optimality consensus method. BMC Struct Biol (2010) 0.81
Betaalpha-hairpin clamps brace betaalphabeta modules and can make substantive contributions to the stability of TIM barrel proteins. PLoS One (2009) 0.81
TRPV4 mutations in children with congenital distal spinal muscular atrophy. Neurogenetics (2012) 0.81
An improved hybrid global optimization method for protein tertiary structure prediction. Comput Optim Appl (2010) 0.80
The plant proteome folding project: structure and positive selection in plant protein families. Genome Biol Evol (2012) 0.79
Molecular modeling of phosphorylation sites in proteins using a database of local structure segments. J Mol Model (2005) 0.79
Motif-directed redesign of enzyme specificity. Protein Sci (2014) 0.79
Computational tools for rational protein engineering of aldolases. Comput Struct Biotechnol J (2012) 0.79
Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA). PLoS One (2009) 0.79
Sampling multiple scoring functions can improve protein loop structure prediction accuracy. J Chem Inf Model (2011) 0.78
Support-vector-machine classification of linear functional motifs in proteins. J Mol Model (2005) 0.78
Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. J Chem Theory Comput (2013) 0.78
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
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci (2002) 5.47
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
MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res (2009) 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
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
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
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
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