Published in Proteins on August 23, 2011
Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10. Proteins (2013) 2.09
High-resolution comparative modeling with RosettaCM. Structure (2013) 1.96
I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res (2015) 1.59
Biochemical analysis of the role of G118R-linked dolutegravir drug resistance substitutions in HIV-1 integrase. Antimicrob Agents Chemother (2013) 1.21
H2S and NO cooperatively regulate vascular tone by activating a neuroendocrine HNO-TRPA1-CGRP signalling pathway. Nat Commun (2014) 1.16
Evaluation of predictions in the CASP10 model refinement category. Proteins (2014) 1.15
Toward optimal fragment generations for ab initio protein structure assembly. Proteins (2012) 1.13
GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Res (2013) 1.06
Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface (2012) 1.01
A position-specific distance-dependent statistical potential for protein structure and functional study. Structure (2012) 0.99
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. Bioinformatics (2013) 0.95
A conformation ensemble approach to protein residue-residue contact. BMC Struct Biol (2011) 0.94
Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr Opin Struct Biol (2013) 0.93
Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics (2013) 0.90
PI(2)PE: A Suite of Web Servers for Predictions Ranging From Protein Structure to Binding Kinetics. Biophys Rev (2012) 0.88
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins (2015) 0.87
ResQ: An Approach to Unified Estimation of B-Factor and Residue-Specific Error in Protein Structure Prediction. J Mol Biol (2015) 0.87
Homology modeling of larger proteins guided by chemical shifts. Nat Methods (2015) 0.86
An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. PLoS Comput Biol (2013) 0.85
Protein Structure and Function Prediction Using I-TASSER. Curr Protoc Bioinformatics (2015) 0.82
Evidence supporting the existence of a NUPR1-like family of helix-loop-helix chromatin proteins related to, yet distinct from, AT hook-containing HMG proteins. J Mol Model (2014) 0.82
What is the best reference state for designing statistical atomic potentials in protein structure prediction? Proteins (2012) 0.81
Membrane proteins: always an insoluble problem? Biochem Soc Trans (2016) 0.81
How good are simplified models for protein structure prediction? Adv Bioinformatics (2014) 0.80
Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry (2013) 0.80
Structure and location of the regulatory β subunits in the (αβγδ)4 phosphorylase kinase complex. J Biol Chem (2012) 0.80
Low-resolution structure of the full-length barley (Hordeum vulgare) SGT1 protein in solution, obtained using small-angle X-ray scattering. PLoS One (2014) 0.79
Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. PLoS One (2013) 0.78
Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering. Open Biol (2015) 0.78
Computational enzyme design approaches with significant biological outcomes: progress and challenges. Comput Struct Biotechnol J (2012) 0.78
Design of symmetric TIM barrel proteins from first principles. BMC Biochem (2015) 0.78
Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins. Genome Biol Evol (2013) 0.77
Insights from molecular dynamics simulations: structural basis for the V567D mutation-induced instability of zebrafish alpha-dystroglycan and comparison with the murine model. PLoS One (2014) 0.77
Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization. BMC Bioinformatics (2012) 0.77
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana. BMC Bioinformatics (2012) 0.77
LabCaS: labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields. Proteins (2012) 0.76
KECSA-Movable Type Implicit Solvation Model (KMTISM). J Chem Theory Comput (2015) 0.76
Assessment of 3D models for allergen research. Proteins (2013) 0.76
Mass spectrometry coupled experiments and protein structure modeling methods. Int J Mol Sci (2013) 0.76
Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement. PLoS One (2014) 0.76
Structural insights into the folding defects of oncogenic pVHL lead to correction of its function in vitro. PLoS One (2013) 0.76
Functional and Spectroscopic Characterization of Chlamydomonas reinhardtii Truncated Hemoglobins. PLoS One (2015) 0.76
The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches. Int J Mol Sci (2014) 0.76
Cysteine-Rich Atrial Secretory Protein from the Snail Achatina achatina: Purification and Structural Characterization. PLoS One (2015) 0.75
Multi-Dimensional Scaling and MODELLER-Based Evolutionary Algorithms for Protein Model Refinement. Proc Congr Evol Comput (2014) 0.75
Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding. Retrovirology (2014) 0.75
PCP-ML: protein characterization package for machine learning. BMC Res Notes (2014) 0.75
Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods? J Phys Chem B (2016) 0.75
A comparison of different functions for predicted protein model quality assessment. J Comput Aided Mol Des (2016) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
Protein homology detection by HMM-HMM comparison. Bioinformatics (2004) 21.92
I-TASSER server for protein 3D structure prediction. BMC Bioinformatics (2008) 18.28
Satisfying hydrogen bonding potential in proteins. J Mol Biol (1994) 14.79
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res (2005) 14.15
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
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
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
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
Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol (1991) 3.81
Assessment of CASP7 predictions for template-based modeling targets. Proteins (2007) 3.50
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
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (2011) 2.97
3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins (2003) 2.91
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
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins (2005) 2.72
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins (2003) 2.67
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
Evaluation of template-based models in CASP8 with standard measures. Proteins (2009) 2.46
Protein threading using PROSPECT: design and evaluation. Proteins (2000) 2.26
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins (2004) 2.16
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08
Assessment of CASP7 structure predictions for template free targets. Proteins (2007) 1.98
Assessment of CASP8 structure predictions for template free targets. Proteins (2009) 1.96
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res (2005) 1.95
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
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 multi-template combination algorithm for protein comparative modeling. BMC Struct Biol (2008) 1.62
ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J (2003) 1.47
MUFOLD: A new solution for protein 3D structure prediction. Proteins (2010) 1.42
Computational methods in protein structure prediction. Biotechnol Bioeng (2007) 1.39
Improving protein structure prediction using multiple sequence-based contact predictions. Structure (2011) 1.24
Boosting Protein Threading Accuracy. Res Comput Mol Biol (2009) 1.17
Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics (2005) 1.16
HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. PLoS One (2009) 1.02
Recognizing protein substructure similarity using segmental threading. Structure (2010) 0.91
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
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential. Bioinformatics (2009) 0.78
I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc (2010) 22.66
PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res (2004) 19.62
The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res (2002) 12.20
The Protein Information Resource. Nucleic Acids Res (2003) 11.17
PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res (2009) 11.05
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One (2011) 5.64
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res (2007) 5.30
The pediatric preclinical testing program: description of models and early testing results. Pediatr Blood Cancer (2007) 5.28
Adeno-associated virus serotype 8 efficiently delivers genes to muscle and heart. Nat Biotechnol (2005) 5.27
Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol (2007) 5.07
An overview of the PubChem BioAssay resource. Nucleic Acids Res (2009) 4.75
Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc Natl Acad Sci U S A (2008) 4.07
IL-21 regulates germinal center B cell differentiation and proliferation through a B cell-intrinsic mechanism. J Exp Med (2010) 4.04
Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. Nat Genet (2010) 4.01
Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell (2004) 3.98
PubChem's BioAssay Database. Nucleic Acids Res (2011) 3.74
The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res (2010) 3.74
RET fusions define a unique molecular and clinicopathologic subtype of non-small-cell lung cancer. J Clin Oncol (2012) 3.72
BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics (2005) 3.43
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins (2008) 3.38
CXCL12 / CXCR4 / CXCR7 chemokine axis and cancer progression. Cancer Metastasis Rev (2010) 3.24
How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (2010) 3.22
Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A (2007) 3.06
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure (2011) 2.97
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins (2012) 2.94
Three-field or two-field resection for thoracic esophageal cancer: a meta-analysis. Ann Thorac Surg (2013) 2.92
Coordination of Rab8 and Rab11 in primary ciliogenesis. Proc Natl Acad Sci U S A (2010) 2.88
S-nitrosohemoglobin deficiency: a mechanism for loss of physiological activity in banked blood. Proc Natl Acad Sci U S A (2007) 2.77
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Res (2012) 2.75
Long noncoding RNAs with snoRNA ends. Mol Cell (2012) 2.71
Identification of the enzymatic mechanism of nitroglycerin bioactivation. Proc Natl Acad Sci U S A (2002) 2.65
Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework. Inorg Chem (2007) 2.57
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res (2012) 2.56
Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy. Analyst (2008) 2.45
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (2013) 2.43
Chibby, a nuclear beta-catenin-associated antagonist of the Wnt/Wingless pathway. Nature (2003) 2.42
Functional mesenchymal stem cells derived from human induced pluripotent stem cells attenuate limb ischemia in mice. Circulation (2010) 2.39
Autophagy negatively regulates Wnt signalling by promoting Dishevelled degradation. Nat Cell Biol (2010) 2.37
Arsenic detoxification and evolution of trimethylarsine gas by a microbial arsenite S-adenosylmethionine methyltransferase. Proc Natl Acad Sci U S A (2006) 2.37
MicroRNA-101 inhibited postinfarct cardiac fibrosis and improved left ventricular compliance via the FBJ osteosarcoma oncogene/transforming growth factor-β1 pathway. Circulation (2012) 2.36
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins (2004) 2.34
The yak genome and adaptation to life at high altitude. Nat Genet (2012) 2.34
Characterization of sleep in zebrafish and insomnia in hypocretin receptor mutants. PLoS Biol (2007) 2.34
Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophys J (2011) 2.24
Early detection of lung adenocarcinoma in sputum by a panel of microRNA markers. Int J Cancer (2010) 2.20
An essential role for mitochondrial aldehyde dehydrogenase in nitroglycerin bioactivation. Proc Natl Acad Sci U S A (2005) 2.18
Dual-modality monitoring of targeted intraarterial delivery of mesenchymal stem cells after transient ischemia. Stroke (2008) 2.18
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (2004) 2.17
HAb18G/CD147 promotes activation of hepatic stellate cells and is a target for antibody therapy of liver fibrosis. J Hepatol (2012) 2.15
PubChem BioAssay: 2014 update. Nucleic Acids Res (2013) 2.14
Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. Nat Genet (2011) 2.13
14-3-3zeta Cooperates with ErbB2 to promote ductal carcinoma in situ progression to invasive breast cancer by inducing epithelial-mesenchymal transition. Cancer Cell (2009) 2.09
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (2008) 2.08
Pattern of lymphatic spread in thoracic esophageal squamous cell carcinoma: A single-institution experience. J Thorac Cardiovasc Surg (2012) 2.08
Exo70 interacts with phospholipids and mediates the targeting of the exocyst to the plasma membrane. EMBO J (2007) 2.03
Human epithelial cancers secrete immunoglobulin g with unidentified specificity to promote growth and survival of tumor cells. Cancer Res (2003) 2.00
Membrane association and functional regulation of Sec3 by phospholipids and Cdc42. J Cell Biol (2008) 1.99
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat Chem Biol (2008) 1.96
DNA-nanoparticle superlattices formed from anisotropic building blocks. Nat Mater (2010) 1.92
Monocyte chemotactic protein-1 (MCP-1) acts as a paracrine and autocrine factor for prostate cancer growth and invasion. Prostate (2006) 1.90
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins (2009) 1.89
Synthesis, structure, and luminescent properties of hybrid inorganic-organic framework materials formed by lead aromatic carboxylates: inorganic connectivity variation from 0D to 3D. Inorg Chem (2009) 1.85
LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis. Plant Physiol (2008) 1.79
Monocyte chemotactic protein-1 mediates prostate cancer-induced bone resorption. Cancer Res (2007) 1.79
Autophagy is a therapeutic target in anticancer drug resistance. Biochim Biophys Acta (2010) 1.77
PI3K pathway activation results in low efficacy of both trastuzumab and lapatinib. BMC Cancer (2011) 1.73
Overweight is associated with decreased cognitive functioning among school-age children and adolescents. Obesity (Silver Spring) (2008) 1.71
Exo70 interacts with the Arp2/3 complex and regulates cell migration. Nat Cell Biol (2006) 1.70
The RABIT: a rapid automated biodosimetry tool for radiological triage. Health Phys (2010) 1.69
The role of concurrent chemoradiotherapy in the treatment of locoregionally advanced nasopharyngeal carcinoma among endemic population: a meta-analysis of the phase III randomized trials. BMC Cancer (2010) 1.68
CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS One (2012) 1.68
A multicenter, randomized, double-blind, parallel-group, placebo-controlled study of the effects of qili qiangxin capsules in patients with chronic heart failure. J Am Coll Cardiol (2013) 1.66
Very high fructose intake increases serum LDL-cholesterol and total cholesterol: a meta-analysis of controlled feeding trials. J Nutr (2013) 1.65
Findings from 2010 Global Adult Tobacco Survey: implementation of MPOWER policy in China. Biomed Environ Sci (2010) 1.65
Gram-scale synthesis of submicrometer-long polythiophene wires in mesoporous silica matrices. Angew Chem Int Ed Engl (2003) 1.64
Associations between body mass index and the prevalence of low micronutrient levels among US adults. MedGenMed (2006) 1.63
IL-4 and IL-12 regulate proteoglycan-induced arthritis through Stat-dependent mechanisms. J Immunol (2002) 1.61
The neocarzinostatin biosynthetic gene cluster from Streptomyces carzinostaticus ATCC 15944 involving two iterative type I polyketide synthases. Chem Biol (2005) 1.61
BETA2/NeuroD1 null mice: a new model for transcription factor-dependent photoreceptor degeneration. J Neurosci (2003) 1.61
Outcomes of the POG 9340/9341/9342 trials for children with high-risk neuroblastoma: a report from the Children's Oncology Group. Pediatr Blood Cancer (2008) 1.60
Inhibition of interleukin-6 with CNTO328, an anti-interleukin-6 monoclonal antibody, inhibits conversion of androgen-dependent prostate cancer to an androgen-independent phenotype in orchiectomized mice. Cancer Res (2006) 1.59
Control of autophagy maturation by acid sphingomyelinase in mouse coronary arterial smooth muscle cells: protective role in atherosclerosis. J Mol Med (Berl) (2014) 1.59
Involvement of human natural killer cells in asthma pathogenesis: natural killer 2 cells in type 2 cytokine predominance. J Allergy Clin Immunol (2005) 1.59
SUMO1 modification of PTEN regulates tumorigenesis by controlling its association with the plasma membrane. Nat Commun (2012) 1.58
Bone morphogenetic protein-6 promotes osteoblastic prostate cancer bone metastases through a dual mechanism. Cancer Res (2005) 1.56
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
Dendrite-free lithium deposition via self-healing electrostatic shield mechanism. J Am Chem Soc (2013) 1.56
FGF21 and the late adaptive response to starvation in humans. J Clin Invest (2015) 1.55
Palladium-catalyzed enantioselective addition of two distinct nucleophiles across alkenes capable of quinone methide formation. J Am Chem Soc (2009) 1.54
4,4'-Thiodipyridinium tetrachlorocopper(II). Acta Crystallogr C (2004) 1.54
Generating triangulated macromolecular surfaces by Euclidean Distance Transform. PLoS One (2009) 1.54
Postsynaptically synthesized prostaglandin E2 (PGE2) modulates hippocampal synaptic transmission via a presynaptic PGE2 EP2 receptor. J Neurosci (2005) 1.52
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell (2012) 1.52
TRAIL death receptor 4 signaling via lysosome fusion and membrane raft clustering in coronary arterial endothelial cells: evidence from ASM knockout mice. J Mol Med (Berl) (2012) 1.52
No-reflow protection and long-term efficacy for acute myocardial infarction with Tongxinluo: a randomized double-blind placebo-controlled multicenter clinical trial (ENLEAT Trial). Chin Med J (Engl) (2010) 1.51
Increased susceptibility to liver injury in hepatitis B virus transgenic mice involves NKG2D-ligand interaction and natural killer cells. Hepatology (2007) 1.49
HAb18G/CD147 functions in invasion and metastasis of hepatocellular carcinoma. Mol Cancer Res (2007) 1.48