Published in PLoS Biol on April 01, 2007
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
Protein structure prediction: when is it useful? Curr Opin Struct Biol (2009) 2.52
The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis. Cell (2013) 1.46
The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nature (2015) 1.24
Boosting the prediction and understanding of DNA-binding domains from sequence. Nucleic Acids Res (2010) 1.02
The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Res (2011) 0.98
Deciphering diatom biochemical pathways via whole-cell proteomics. Aquat Microb Ecol (2009) 0.98
Asynchronous replica exchange for molecular simulations. J Comput Chem (2008) 0.97
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics (2013) 0.95
Evidence for the robustness of protein complexes to inter-species hybridization. PLoS Genet (2012) 0.90
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep (2013) 0.88
Highly abundant proteins favor more stable 3D structures in yeast. Biophys J (2013) 0.88
FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res (2008) 0.87
BUD22 affects Ty1 retrotransposition and ribosome biogenesis in Saccharomyces cerevisiae. Genetics (2010) 0.86
A novel N-terminal domain may dictate the glucose response of Mondo proteins. PLoS One (2012) 0.84
PSPP: a protein structure prediction pipeline for computing clusters. PLoS One (2009) 0.83
In silico evidence for functional specialization after genome duplication in yeast. FEMS Yeast Res (2009) 0.83
Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. J Biol Chem (2013) 0.80
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PLoS Comput Biol (2011) 0.78
Molecular Characterization and Functional Analysis of Cytochrome b5 Reductase (CBR) Encoding Genes from the Carotenogenic Yeast Xanthophyllomyces dendrorhous. PLoS One (2015) 0.75
Science wikinomics. Mass networking through the web creates new forms of scientific collaboration. EMBO Rep (2009) 0.75
Complete fold annotation of the human proteome using a novel structural feature space. Sci Rep (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res (1999) 40.62
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol (2001) 15.97
A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol (1998) 14.18
SCOP: a structural classification of proteins database. Nucleic Acids Res (2000) 14.14
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
Protein structure prediction using Rosetta. Methods Enzymol (2004) 12.05
The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res (2000) 11.38
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol (1997) 10.38
The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03
Toward high-resolution de novo structure prediction for small proteins. Science (2005) 9.18
3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci (2002) 5.47
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins (1999) 4.86
Assigning function to yeast proteins by integration of technologies. Mol Cell (2003) 4.58
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2006) 3.59
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol (1999) 3.46
Automated prediction of CASP-5 structures using the Robetta server. Proteins (2003) 3.41
Identification of a translation initiation factor 3 (eIF3) core complex, conserved in yeast and mammals, that interacts with eIF5. Mol Cell Biol (1998) 2.91
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
The Yeast Resource Center Public Data Repository. Nucleic Acids Res (2005) 2.19
A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res (2004) 2.15
Free modeling with Rosetta in CASP6. Proteins (2005) 2.10
Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins (2001) 2.07
Contact order and ab initio protein structure prediction. Protein Sci (2002) 1.59
Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins (2001) 1.54
Insights into ATP synthase assembly and function through the molecular genetic manipulation of subunits of the yeast mitochondrial enzyme complex. Biochim Biophys Acta (2000) 1.41
Detection of reliable and unexpected protein fold predictions using 3D-Jury. Nucleic Acids Res (2003) 1.35
Mitochondrial ribosomal proteins (MRPs) of yeast. Biochem J (1998) 1.29
Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins (2001) 1.26
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol (2004) 1.25
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins (2005) 1.17
Extended N-terminal sequencing of proteins of the large ribosomal subunit from yeast mitochondria. FEBS Lett (1991) 1.05
Formation of the yeast F1F0-ATP synthase dimeric complex does not require the ATPase inhibitor protein, Inh1. J Biol Chem (2002) 1.05
Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae. Eur J Biochem (1997) 0.95
2DDB - a bioinformatics solution for analysis of quantitative proteomics data. BMC Bioinformatics (2006) 0.93
Proteomic 2DE database for spot selection, automated annotation, and data analysis. J Proteome Res (2003) 0.84
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
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc Natl Acad Sci U S A (2010) 5.59
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
A validated regulatory network for Th17 cell specification. Cell (2012) 4.82
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
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell (2012) 4.21
Computational redesign of endonuclease DNA binding and cleavage specificity. Nature (2006) 4.06
The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics (2006) 4.05
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
Phosphoregulation and depolymerization-driven movement of the Dam1 complex do not require ring formation. Nat Cell Biol (2008) 3.16
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
The Ndc80 kinetochore complex forms load-bearing attachments to dynamic microtubule tips via biased diffusion. Cell (2009) 2.79
Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins (2003) 2.77
BioNetBuilder: automatic integration of biological networks. Bioinformatics (2006) 2.76
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75
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
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
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
Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol (2012) 2.40
The Dam1 kinetochore complex harnesses microtubule dynamics to produce force and movement. Proc Natl Acad Sci U S A (2006) 2.40
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