Published in Curr Opin Struct Biol on April 22, 2008
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
I-TASSER: fully automated protein structure prediction in CASP8. Proteins (2009) 3.21
Protein structure prediction: when is it useful? Curr Opin Struct Biol (2009) 2.52
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA (2009) 1.78
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins (2011) 1.58
Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately. Proc Natl Acad Sci U S A (2010) 1.51
Nanostructure and molecular mechanics of spider dragline silk protein assemblies. J R Soc Interface (2010) 1.46
Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44
Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (2011) 1.34
Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol (2010) 1.33
CASP10 results compared to those of previous CASP experiments. Proteins (2013) 1.32
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics (2010) 1.30
Crystal structure of folliculin reveals a hidDENN function in genetically inherited renal cancer. Open Biol (2012) 1.29
KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res (2012) 1.25
Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res (2010) 1.18
Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16
BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins (2011) 1.08
Template-based structure modeling of protein-protein interactions. Curr Opin Struct Biol (2013) 1.08
GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res (2012) 1.08
Protein structure prediction and model quality assessment. Drug Discov Today (2009) 1.07
Biomolecularmodeling and simulation: a field coming of age. Q Rev Biophys (2011) 1.06
ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (2013) 1.05
Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics (2012) 1.04
ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. PLoS One (2008) 1.02
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics (2009) 1.02
Protein folding and de novo protein design for biotechnological applications. Trends Biotechnol (2013) 1.02
Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface (2012) 1.01
From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci (2013) 1.00
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem (2012) 0.99
FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. Mol Pharm (2012) 0.98
Template-based protein structure modeling using TASSER(VMT.). Proteins (2011) 0.98
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
Structural determinants of limited proteolysis. J Proteome Res (2011) 0.95
Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery. Comput Struct Biotechnol J (2013) 0.95
Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors. Nat Commun (2015) 0.95
A conformation ensemble approach to protein residue-residue contact. BMC Struct Biol (2011) 0.94
How many protein-protein interactions types exist in nature? PLoS One (2012) 0.94
The study of protein conformation in solution via direct sampling by desorption electrospray ionization mass spectrometry. J Am Soc Mass Spectrom (2010) 0.94
Computational protein design and large-scale assessment by I-TASSER structure assembly simulations. J Mol Biol (2011) 0.94
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics (2011) 0.93
The MULTICOM toolbox for protein structure prediction. BMC Bioinformatics (2012) 0.93
Large-scale model quality assessment for improving protein tertiary structure prediction. Bioinformatics (2015) 0.93
Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophys J (2010) 0.92
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. BMC Bioinformatics (2012) 0.92
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets. Proc Natl Acad Sci U S A (2013) 0.92
KATP channel Kir6.2 E23K variant overrepresented in human heart failure is associated with impaired exercise stress response. Hum Genet (2009) 0.92
Recognizing protein substructure similarity using segmental threading. Structure (2010) 0.91
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J Comput Chem (2011) 0.90
Systems biology in the context of big data and networks. Biomed Res Int (2014) 0.90
Transmembrane topology of the mammalian Slc11a2 iron transporter. Biochemistry (2009) 0.89
The chromodomain-containing NH(2)-terminus of Chromator interacts with histone H1 and is required for correct targeting to chromatin. Chromosoma (2011) 0.89
A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. J Chem Theory Comput (2009) 0.88
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). BMC Bioinformatics (2013) 0.88
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep (2013) 0.88
FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res (2008) 0.87
Identification of ligand templates using local structure alignment for structure-based drug design. J Chem Inf Model (2012) 0.87
Selecting high quality protein structures from diverse conformational ensembles. Biophys J (2009) 0.86
Contact prediction for beta and alpha-beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO-FOLD. Proteins (2010) 0.85
Single-molecule studies of riboswitch folding. Biochim Biophys Acta (2014) 0.85
Prediction of conformational changes by single mutation in the hepatitis B virus surface antigen (HBsAg) identified in HBsAg-negative blood donors. Virol J (2010) 0.85
Structural features that predict real-value fluctuations of globular proteins. Proteins (2012) 0.85
Effective inter-residue contact definitions for accurate protein fold recognition. BMC Bioinformatics (2012) 0.84
Effect of using suboptimal alignments in template-based protein structure prediction. Proteins (2011) 0.84
EvoDesign: De novo protein design based on structural and evolutionary profiles. Nucleic Acids Res (2013) 0.84
Rampant historical mitochondrial genome introgression between two species of green pond frogs, Pelophylax nigromaculatus and P. plancyi. BMC Evol Biol (2010) 0.84
An iterative self-refining and self-evaluating approach for protein model quality estimation. Protein Sci (2011) 0.83
Fast geometric consensus approach for protein model quality assessment. J Comput Biol (2011) 0.83
Norbin: A promising central nervous system regulator. Commun Integr Biol (2010) 0.82
ASTRO-FOLD 2.0: an Enhanced Framework for Protein Structure Prediction. AIChE J (2011) 0.82
Structure of Debaryomyces castellii CBS 2923 phytase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.82
Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches. J Mol Model (2011) 0.82
Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes. J Bacteriol (2011) 0.82
Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening. Methods (2014) 0.81
Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in Drosophila. Nucleic Acids Res (2014) 0.81
β-sheet topology prediction with high precision and recall for β and mixed α/β proteins. PLoS One (2012) 0.81
Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins. Mol Cell Proteomics (2012) 0.81
Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11. Proteins (2015) 0.81
Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. BMC Bioinformatics (2014) 0.80
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallogr D Struct Biol (2016) 0.80
Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding. Sci Rep (2015) 0.80
STRUM: structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics (2016) 0.79
Evaluating mixture models for building RNA knowledge-based potentials. J Bioinform Comput Biol (2012) 0.79
Computational tools for epitope vaccine design and evaluation. Curr Opin Virol (2015) 0.79
Refinement by shifting secondary structure elements improves sequence alignments. Proteins (2015) 0.79
Beauveria bassiana Lipase A expressed in Komagataella (Pichia) pastoris with potential for biodiesel catalysis. Front Microbiol (2015) 0.79
When the lowest energy does not induce native structures: parallel minimization of multi-energy values by hybridizing searching intelligences. PLoS One (2012) 0.79
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol (2016) 0.78
Hofmeister salts recover a misfolded multiprotein complex for subsequent structural measurements in the gas phase. Angew Chem Int Ed Engl (2013) 0.78
A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognit Lett (2010) 0.78
General overview on structure prediction of twilight-zone proteins. Theor Biol Med Model (2015) 0.78
Computational enzyme design approaches with significant biological outcomes: progress and challenges. Comput Struct Biotechnol J (2012) 0.78
Odorant receptors of Drosophila are sensitive to the molecular volume of odorants. Sci Rep (2016) 0.77
The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment. F1000Res (2013) 0.77
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11. Proteins (2015) 0.77
Prediction of peptide reactivity with human IVIg through a knowledge-based approach. PLoS One (2011) 0.77
Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure. BMC Struct Biol (2013) 0.77
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A (1987) 29.26
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
A method to identify protein sequences that fold into a known three-dimensional structure. Science (1991) 14.08
Scoring function for automated assessment of protein structure template quality. Proteins (2004) 10.99
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol (1997) 10.38
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol (2001) 10.02
Toward high-resolution de novo structure prediction for small proteins. Science (2005) 9.18
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (1998) 8.46
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol (2003) 8.35
A new approach to protein fold recognition. Nature (1992) 8.17
3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics (2003) 7.99
Template-based modeling and free modeling by I-TASSER in CASP7. Proteins (2007) 6.45
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol (1999) 6.42
Structural genomics: beyond the human genome project. Nat Genet (1999) 5.58
Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A (2004) 5.44
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
The impact of structural genomics: expectations and outcomes. Science (2006) 5.30
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res (2005) 4.99
TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J (2003) 4.62
MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2006) 3.56
Assessment of CASP7 predictions for template-based modeling targets. Proteins (2007) 3.50
Automated server predictions in CASP7. Proteins (2007) 3.40
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
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins (2007) 3.01
3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins (2003) 2.91
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol (2002) 2.73
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins (2005) 2.72
CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins (2003) 2.60
Critical assessment of methods of protein structure prediction (CASP)--round 6. Proteins (2005) 2.58
Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins (2007) 2.50
Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci U S A (2006) 2.47
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins (2004) 2.34
Assessment of homology-based predictions in CASP5. Proteins (2003) 2.29
Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins (2005) 2.27
Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci U S A (2007) 2.12
Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins (2007) 1.83
An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci U S A (1994) 1.83
A machine learning information retrieval approach to protein fold recognition. Bioinformatics (2006) 1.75
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res (2003) 1.71
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J Comput Chem (2007) 1.71
Servers for protein structure prediction. Curr Opin Struct Biol (2006) 1.70
Molecular dynamics in the endgame of protein structure prediction. J Mol Biol (2001) 1.69
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci U S A (2005) 1.65
LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci (2005) 1.38
Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins (2005) 1.18