Published in Proc Natl Acad Sci U S A on May 04, 2004
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
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A (2007) 3.87
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
I-TASSER: fully automated protein structure prediction in CASP8. Proteins (2009) 3.21
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A (2007) 3.15
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94
On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci U S A (2006) 2.85
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem (2008) 2.58
Protein structure prediction: when is it useful? Curr Opin Struct Biol (2009) 2.52
Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol (2006) 2.40
Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A (2010) 2.22
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J (2004) 2.13
Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10. Proteins (2013) 2.09
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08
Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics (2007) 2.03
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res (2008) 1.68
Genomics-aided structure prediction. Proc Natl Acad Sci U S A (2012) 1.63
A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol (2008) 1.62
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
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PLoS One (2010) 1.56
Optimal mutation sites for PRE data collection and membrane protein structure prediction. Structure (2011) 1.55
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci (2008) 1.45
NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res (2009) 1.43
MUFOLD: A new solution for protein 3D structure prediction. Proteins (2010) 1.42
Organelle tethering by a homotypic PDZ interaction underlies formation of the Golgi membrane network. J Cell Biol (2009) 1.36
Alternative splicing and protein structure evolution. Nucleic Acids Res (2007) 1.35
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem (2008) 1.34
Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (2011) 1.34
FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform (2009) 1.33
Ab initio protein structure prediction using chunk-TASSER. Biophys J (2007) 1.32
Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J (2004) 1.28
Improving protein structure prediction using multiple sequence-based contact predictions. Structure (2011) 1.24
Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction. Structure (2009) 1.23
RNA and protein 3D structure modeling: similarities and differences. J Mol Model (2011) 1.19
Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A (2008) 1.18
Development of a physics-based force field for the scoring and refinement of protein models. Biophys J (2008) 1.17
Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins (2008) 1.16
Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16
Toward optimal fragment generations for ab initio protein structure assembly. Proteins (2012) 1.13
Protein structure prediction by pro-Sp3-TASSER. Biophys J (2009) 1.12
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model (2012) 1.09
BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins (2011) 1.08
M-TASSER: an algorithm for protein quaternary structure prediction. Biophys J (2007) 1.08
Further evidence for the likely completeness of the library of solved single domain protein structures. J Phys Chem B (2012) 1.07
MESSA: MEta-Server for protein Sequence Analysis. BMC Biol (2012) 1.06
Avl9p, a member of a novel protein superfamily, functions in the late secretory pathway. Mol Biol Cell (2007) 1.05
Probing protein fold space with a simplified model. J Mol Biol (2007) 1.03
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J (2008) 1.03
TASSER-Lite: an automated tool for protein comparative modeling. Biophys J (2006) 1.03
Quality assessment of protein model-structures using evolutionary conservation. Bioinformatics (2010) 1.01
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (2010) 1.01
Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface (2012) 1.01
Interplay of physics and evolution in the likely origin of protein biochemical function. Proc Natl Acad Sci U S A (2013) 1.01
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins (2010) 1.00
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem (2010) 0.99
Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Sci Rep (2015) 0.99
Template-based protein structure modeling using TASSER(VMT.). Proteins (2011) 0.98
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Comput Biol (2009) 0.98
FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. Mol Pharm (2012) 0.98
Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment. BMC Struct Biol (2014) 0.97
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins (2010) 0.97
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep (2013) 0.97
FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins (2010) 0.95
Performance of the Pro-sp3-TASSER server in CASP8. Proteins (2009) 0.95
Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr Opin Struct Biol (2013) 0.93
KATP channel Kir6.2 E23K variant overrepresented in human heart failure is associated with impaired exercise stress response. Hum Genet (2009) 0.92
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. Phys Chem Chem Phys (2011) 0.91
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model (2010) 0.91
CLE14/CLE20 peptides may interact with CLAVATA2/CORYNE receptor-like kinases to irreversibly inhibit cell division in the root meristem of Arabidopsis. Planta (2010) 0.91
Recognizing protein substructure similarity using segmental threading. Structure (2010) 0.91
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation. Proteins (2009) 0.90
GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome. Structure (2015) 0.90
Generalized pattern search algorithm for Peptide structure prediction. Biophys J (2008) 0.89
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol (2013) 0.89
Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Sci Rep (2013) 0.88
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
Structure-based classification of 45 FK506-binding proteins. Proteins (2008) 0.88
Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biol (2013) 0.87
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins (2015) 0.87
Constructing templates for protein structure prediction by simulation of protein folding pathways. Proteins (2008) 0.87
Putting the pathway back into protein folding. Proc Natl Acad Sci U S A (2005) 0.86
Altering coenzyme specificity of Pichia stipitis xylose reductase by the semi-rational approach CASTing. Microb Cell Fact (2007) 0.86
Selecting high quality protein structures from diverse conformational ensembles. Biophys J (2009) 0.86
A new drug design targeting the adenosinergic system for Huntington's disease. PLoS One (2011) 0.85
eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS One (2012) 0.85
Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers. BMC Struct Biol (2010) 0.84
Protein Structure and Function Prediction Using I-TASSER. Curr Protoc Bioinformatics (2015) 0.82
Targeting protein-protein interactions for parasite control. PLoS One (2011) 0.82
Recursive protein modeling: a divide and conquer strategy for Protein Structure Prediction and its case study in CASP9. J Bioinform Comput Biol (2012) 0.82
Structure prediction and binding sites analysis of curcin protein of Jatropha curcas using computational approaches. J Mol Model (2011) 0.82
The outlook for protein engineering in crop improvement. Plant Physiol (2008) 0.81
aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species. BMC Microbiol (2009) 0.81
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TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
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How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol (2003) 6.16
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem (2004) 4.87
TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J (2003) 4.62
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A (2007) 3.15
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins (2002) 3.09
On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci U S A (2006) 2.85
The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A (2005) 2.75
Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem (2008) 2.58
TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins (2005) 2.57
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins (2002) 2.42
Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol (2006) 2.40
The PDB is a covering set of small protein structures. J Mol Biol (2003) 2.26
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion. Proc Natl Acad Sci U S A (2010) 2.22
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J (2004) 2.13
Analysis of TASSER-based CASP7 protein structure prediction results. Proteins (2007) 1.85
Development of unified statistical potentials describing protein-protein interactions. Biophys J (2003) 1.83
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
EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res (2004) 1.70
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res (2008) 1.68
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics (2008) 1.50
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins (2004) 1.41
Efficient prediction of nucleic acid binding function from low-resolution protein structures. J Mol Biol (2006) 1.40
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC Bioinformatics (2009) 1.40
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J (2011) 1.39
FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol (2009) 1.38
All-atom ab initio folding of a diverse set of proteins. Structure (2007) 1.36
Identification of metabolites with anticancer properties by computational metabolomics. Mol Cancer (2008) 1.35
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem (2008) 1.34
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc Natl Acad Sci U S A (2010) 1.34
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A (2002) 1.33
Ab initio protein structure prediction using chunk-TASSER. Biophys J (2007) 1.32
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res (2003) 1.32
Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J (2004) 1.28
Protein fragment reconstruction using various modeling techniques. J Comput Aided Mol Des (2003) 1.26
The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS One (2008) 1.25
Prediction of physical protein-protein interactions. Phys Biol (2005) 1.23
Assessment of programs for ligand binding affinity prediction. J Comput Chem (2008) 1.23
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinformatics (2012) 1.23
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. PLoS Comput Biol (2009) 1.19
Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci U S A (2008) 1.18
APoc: large-scale identification of similar protein pockets. Bioinformatics (2013) 1.18
iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (2010) 1.17
Development of a physics-based force field for the scoring and refinement of protein models. Biophys J (2008) 1.17
Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins (2008) 1.16
Protein structure prediction by pro-Sp3-TASSER. Biophys J (2009) 1.12
Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins (2010) 1.11
What is the relationship between the global structures of apo and holo proteins? Proteins (2008) 1.10
TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins (2003) 1.10
TASSER-based refinement of NMR structures. Proteins (2006) 1.09
Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol (2004) 1.09
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model (2012) 1.09
Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils. Environ Microbiol (2007) 1.08
M-TASSER: an algorithm for protein quaternary structure prediction. Biophys J (2007) 1.08
A comprehensive survey of small-molecule binding pockets in proteins. PLoS Comput Biol (2013) 1.04
Marker metabolites can be therapeutic targets as well. Nature (2008) 1.04
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J (2008) 1.03
TASSER-Lite: an automated tool for protein comparative modeling. Biophys J (2006) 1.03
Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations. J Chem Phys (2012) 1.02
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation. Proc Natl Acad Sci U S A (2012) 1.02
PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (2010) 1.01
FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins (2010) 1.00
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem (2010) 0.99
Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers (2003) 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
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. PLoS Comput Biol (2009) 0.98
A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. Biophys J (2003) 0.97
New benchmark metrics for protein-protein docking methods. Proteins (2011) 0.97
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins (2010) 0.97
Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase. Biochemistry (2007) 0.95
Performance of the Pro-sp3-TASSER server in CASP8. Proteins (2009) 0.95
High precision multi-genome scale reannotation of enzyme function by EFICAz. BMC Genomics (2006) 0.94
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model (2010) 0.91
Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions. Proteins (2007) 0.91
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. Phys Chem Chem Phys (2011) 0.91
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol (2013) 0.89
WeFold: a coopetition for protein structure prediction. Proteins (2014) 0.88
Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biol (2013) 0.87
Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. Mol Pharm (2010) 0.86
Benchmarking of TASSER in the ab initio limit. Proteins (2007) 0.86
A scoring function for docking ligands to low-resolution protein structures. J Comput Chem (2005) 0.86
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model. Biophys J (2003) 0.83
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers (2003) 0.82
Use of residual dipolar couplings as restraints in ab initio protein structure prediction. Biopolymers (2003) 0.82
On the importance of hydrodynamic interactions in lipid membrane formation. Biophys J (2013) 0.82
Docking of small ligands to low-resolution and theoretically predicted receptor structures. J Comput Chem (2002) 0.82
TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets. Biophys J (2010) 0.81
Benchmarking of dimeric threading and structure refinement. Proteins (2006) 0.81
Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: algorithm and limitations. J Chem Phys (2013) 0.78
Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper. Biophys J (2002) 0.78
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol (2010) 0.78
Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field. J Comput Chem (2007) 0.77
TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates. Proteins (2010) 0.75
Metabolomics identifies the intersection of phosphoethanolamine with menaquinone-triggered apoptosis in an in vitro model of leukemia. Mol Biosyst (2015) 0.75
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