Published in Proteins on January 01, 2007
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 18.28
The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61
Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc (2009) 5.42
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08
Progress and challenges in protein structure prediction. Curr Opin Struct Biol (2008) 3.48
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38
Critical assessment of methods of protein structure prediction-Round VII. Proteins (2007) 3.23
I-TASSER: fully automated protein structure prediction in CASP8. Proteins (2009) 3.21
Nature of the protein universe. Proc Natl Acad Sci U S A (2009) 2.73
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics (2009) 2.64
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (2011) 2.13
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol (2008) 1.62
I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res (2015) 1.59
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics (2013) 1.50
Target domain definition and classification in CASP8. Proteins (2009) 1.48
A single amino acid difference in human APOBEC3H variants determines HIV-1 Vif sensitivity. J Virol (2009) 1.38
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol (2009) 1.33
FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform (2009) 1.33
IFT27, encoding a small GTPase component of IFT particles, is mutated in a consanguineous family with Bardet-Biedl syndrome. Hum Mol Genet (2014) 1.29
Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Res (2008) 1.28
SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PLoS One (2008) 1.27
EasyModeller: A graphical interface to MODELLER. BMC Res Notes (2010) 1.25
SAMPL4, a blind challenge for computational solvation free energies: the compounds considered. J Comput Aided Mol Des (2014) 1.24
Applying undertaker cost functions to model quality assessment. Proteins (2009) 1.23
Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16
Insights into the binding of Phenyltiocarbamide (PTC) agonist to its target human TAS2R38 bitter receptor. PLoS One (2010) 1.12
Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins (2010) 1.11
Protein structure prediction and model quality assessment. Drug Discov Today (2009) 1.07
Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1. Traffic (2011) 1.05
The SAMPL3 blind prediction challenge: transfer energy overview. J Comput Aided Mol Des (2012) 1.04
Mechanisms of pseudosubstrate inhibition of the anaphase promoting complex by Acm1. EMBO J (2011) 1.01
Modeling of the human rhinovirus C capsid suggests a novel topography with insights on receptor preference and immunogenicity. Virology (2013) 1.00
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
Predicting the accuracy of protein-ligand docking on homology models. J Comput Chem (2011) 0.94
Computational protein design and large-scale assessment by I-TASSER structure assembly simulations. J Mol Biol (2011) 0.94
Assessment of ligand binding site predictions in CASP10. Proteins (2014) 0.93
Reduced APOBEC3H variant anti-viral activities are associated with altered RNA binding activities. PLoS One (2012) 0.92
Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Struct Biol (2008) 0.92
Biophysical characterization of Chlamydia trachomatis CT584 supports its potential role as a type III secretion needle tip protein. Biochemistry (2009) 0.92
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep (2013) 0.88
SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database. J Biomol NMR (2009) 0.88
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics (2011) 0.87
Template-based protein structure modeling. Methods Mol Biol (2010) 0.86
Systems biology of the structural proteome. BMC Syst Biol (2016) 0.84
Protein Structure and Function Prediction Using I-TASSER. Curr Protoc Bioinformatics (2015) 0.82
TIM-Finder: a new method for identifying TIM-barrel proteins. BMC Struct Biol (2009) 0.82
Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches. J Mol Model (2011) 0.82
Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure. PLoS One (2010) 0.81
Structural analysis of hubs in human NR-RTK network. Biol Direct (2011) 0.79
Differences in Signal Activation by LH and hCG are Mediated by the LH/CG Receptor's Extracellular Hinge Region. Front Endocrinol (Lausanne) (2015) 0.78
PDBalert: automatic, recurrent remote homology tracking and protein structure prediction. BMC Struct Biol (2008) 0.78
Structural interpretation of protein-protein interaction network. BMC Struct Biol (2010) 0.77
A novel acyl-CoA beta-transaminase characterized from a metagenome. PLoS One (2011) 0.76
From local structure to a global framework: recognition of protein folds. J R Soc Interface (2014) 0.76
Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6. PLoS Comput Biol (2016) 0.76
Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates. PLoS One (2014) 0.75
Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection. PLoS One (2014) 0.75
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
Phaser crystallographic software. J Appl Crystallogr (2007) 108.34
Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr (2011) 67.55
PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr (2002) 53.61
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics (2005) 34.83
Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr (2005) 29.38
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res (2003) 25.86
Likelihood-enhanced fast rotation functions. Acta Crystallogr D Biol Crystallogr (2004) 23.86
Recent improvements to the PROSITE database. Nucleic Acids Res (2004) 11.89
The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr (2007) 7.72
High-resolution structure prediction and the crystallographic phase problem. Nature (2007) 7.67
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr (2009) 6.47
Recent developments in the PHENIX software for automated crystallographic structure determination. J Synchrotron Radiat (2003) 6.28
Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev Cell (2010) 6.24
Simple algorithm for a maximum-likelihood SAD function. Acta Crystallogr D Biol Crystallogr (2004) 5.77
Automated structure solution with the PHENIX suite. Methods Mol Biol (2008) 5.65
Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc (2009) 5.42
The application of multivariate statistical techniques improves single-wavelength anomalous diffraction phasing. Acta Crystallogr D Biol Crystallogr (2003) 5.16
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (2010) 5.08
Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One (2010) 4.94
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res (2004) 4.30
Recent developments in phasing and structure refinement for macromolecular crystallography. Curr Opin Struct Biol (2009) 4.09
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature (2010) 3.84
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins (2013) 3.78
Assessment of CASP7 predictions for template-based modeling targets. Proteins (2007) 3.50
QMEAN server for protein model quality estimation. Nucleic Acids Res (2009) 3.39
Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis (2009) 3.25
Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallogr D Biol Crystallogr (2008) 3.07
Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallogr D Biol Crystallogr (2007) 3.07
The SWISS-MODEL Repository: new features and functionalities. Nucleic Acids Res (2006) 3.00
DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol (2004) 2.86
Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing. Acta Crystallogr D Biol Crystallogr (2003) 2.77
The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) (2013) 2.76
Improved molecular replacement by density- and energy-guided protein structure optimization. Nature (2011) 2.74
Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res (2006) 2.63
Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol (2005) 2.50
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes Dev (2009) 2.44
Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32
Assessment of template based protein structure predictions in CASP9. Proteins (2011) 2.14
Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus. Nat Genet (2006) 2.08
Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol (2010) 2.04
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res (2008) 2.03
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
Assessment of CASP7 structure predictions for template free targets. Proteins (2007) 1.98
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. Nat Genet (2011) 1.91
DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome Res (2005) 1.91
Structure and dynamics of the ATP-bound open conformation of Hsp70 chaperones. Mol Cell (2012) 1.84
Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One (2012) 1.82
Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol (2004) 1.81
Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Sci Transl Med (2012) 1.78
Control of transcription through intragenic patterns of nucleosome composition. Cell (2005) 1.77
How vitronectin binds PAI-1 to modulate fibrinolysis and cell migration. Nat Struct Biol (2003) 1.76
CASP9 target classification. Proteins (2011) 1.75
Improvement of molecular-replacement models with Sculptor. Acta Crystallogr D Biol Crystallogr (2011) 1.61
Assessment of the assessment: evaluation of the model quality estimates in CASP10. Proteins (2013) 1.60
Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J Mol Biol (2002) 1.60
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics (2012) 1.53
Assessment of disorder predictions in CASP7. Proteins (2007) 1.51
Solution structure of the Kaposi's sarcoma-associated herpesvirus K3 N-terminal domain reveals a Novel E2-binding C4HC3-type RING domain. J Biol Chem (2004) 1.50
A redox switch in angiotensinogen modulates angiotensin release. Nature (2010) 1.50
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics (2013) 1.50
Assessment of ligand-binding residue predictions in CASP9. Proteins (2011) 1.47
The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability. Mol Biol Cell (2006) 1.42
Assessment of intramolecular contact predictions for CASP7. Proteins (2007) 1.40
Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure (2013) 1.39
Crystallography: crystallographic evidence for deviating C3b structure. Nature (2007) 1.38
Molecular basis for the unique role of the AAA+ chaperone ClpV in type VI protein secretion. J Biol Chem (2011) 1.37
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics (2011) 1.36
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol (2009) 1.33
Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res (2009) 1.32
Crystal structure of rab11 in complex with rab11 family interacting protein 2. Structure (2006) 1.32
Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr (2012) 1.28
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins (2009) 1.24
Domain definition and target classification for CASP7. Proteins (2007) 1.23
OpenStructure: a flexible software framework for computational structural biology. Bioinformatics (2010) 1.22
Tissue engineering of cultured skin substitutes. J Cell Mol Med (2005) 1.21
Phaser.MRage: automated molecular replacement. Acta Crystallogr D Biol Crystallogr (2013) 1.20
Automated protein structure homology modeling: a progress report. Pharmacogenomics (2004) 1.19
Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients. J Mol Med (Berl) (2001) 1.19
Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. Methods Mol Biol (2012) 1.18
Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. J Biol Chem (2007) 1.17
Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer grid. J Med Chem (2010) 1.13