Published in PLoS One on October 04, 2013
Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol (2015) 0.77
Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins (2016) 0.75
Principles of protein-protein interactions. Proc Natl Acad Sci U S A (1996) 14.51
The atomic structure of protein-protein recognition sites. J Mol Biol (1999) 12.63
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc (2003) 11.65
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol (2003) 8.35
ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A (1992) 6.86
CAPRI: a Critical Assessment of PRedicted Interactions. Proteins (2003) 6.36
Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol (1997) 4.69
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (2002) 4.54
Analysis of protein-protein interaction sites using surface patches. J Mol Biol (1997) 4.51
Protein-protein docking with backbone flexibility. J Mol Biol (2007) 4.32
Protein docking using spherical polar Fourier correlations. Proteins (2000) 3.60
Protein docking using continuum electrostatics and geometric fit. Protein Eng (2001) 3.48
ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol (2004) 3.18
Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15
Residue frequencies and pairing preferences at protein-protein interfaces. Proteins (2001) 3.09
Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics (2004) 2.93
Prediction of protein-protein interaction sites using patch analysis. J Mol Biol (1997) 2.91
ZRANK: reranking protein docking predictions with an optimized energy function. Proteins (2007) 2.79
A role for surface hydrophobicity in protein-protein recognition. Protein Sci (1994) 2.59
Protein-protein docking benchmark version 3.0. Proteins (2008) 2.54
Integrating statistical pair potentials into protein complex prediction. Proteins (2007) 2.53
Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins (1999) 2.49
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol (1998) 2.30
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins (2005) 2.26
RDOCK: refinement of rigid-body protein docking predictions. Proteins (2003) 2.24
Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins (2001) 2.21
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci U S A (2002) 2.20
Protein binding site prediction using an empirical scoring function. Nucleic Acids Res (2006) 2.19
Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci (2004) 2.11
A novel shape complementarity scoring function for protein-protein docking. Proteins (2003) 2.03
Prediction-based fingerprints of protein-protein interactions. Proteins (2007) 1.92
BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins (2000) 1.76
Prediction of protein--protein interaction sites in heterocomplexes with neural networks. Eur J Biochem (2002) 1.74
Statistical analysis and prediction of protein-protein interfaces. Proteins (2005) 1.65
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins (2005) 1.61
Soft protein-protein docking in internal coordinates. Protein Sci (2002) 1.60
meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics (2007) 1.52
WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins (2006) 1.51
Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins (2005) 1.44
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins (2010) 1.39
Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins (1997) 1.38
An iterative knowledge-based scoring function for protein-protein recognition. Proteins (2008) 1.37
Electrostatics in protein-protein docking. Protein Sci (2002) 1.30
Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins (2006) 1.14
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins (2002) 1.08
Automated prediction of ligand-binding sites in proteins. Proteins (2008) 1.05
DOCKGROUND protein-protein docking decoy set. Bioinformatics (2008) 1.03
Using protein binding site prediction to improve protein docking. Gene (2008) 1.01
Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins (2005) 1.00
Weighted geometric docking: incorporating external information in the rotation-translation scan. Proteins (2003) 0.94
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics (2011) 0.93
Side-chain rotamer transitions at protein-protein interfaces. Proteins (2010) 0.92
ASPDock: protein-protein docking algorithm using atomic solvation parameters model. BMC Bioinformatics (2011) 0.90
Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores. Proteins (2004) 0.90
Modeling protein complexes with BiGGER. Proteins (2003) 0.90
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins (2010) 0.88
A holistic approach to protein docking. Proteins (2007) 0.87
A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng Des Sel (2004) 0.87
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information. Proteins (2003) 0.84
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition. Proteins (2005) 0.79
Aldehyde dehydrogenase 1-positive cancer stem cells mediate metastasis and poor clinical outcome in inflammatory breast cancer. Clin Cancer Res (2009) 4.47
Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc Natl Acad Sci U S A (2010) 2.01
Micromagnetic selection of aptamers in microfluidic channels. Proc Natl Acad Sci U S A (2009) 1.66
Aptamer-functionalized Au nanoparticles for the amplified optical detection of thrombin. J Am Chem Soc (2004) 1.64
Continuous, real-time monitoring of cocaine in undiluted blood serum via a microfluidic, electrochemical aptamer-based sensor. J Am Chem Soc (2009) 1.63
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Optimization of electrochemical aptamer-based sensors via optimization of probe packing density and surface chemistry. Langmuir (2008) 1.40
High specificity, electrochemical sandwich assays based on single aptamer sequences and suitable for the direct detection of small-molecule targets in blood and other complex matrices. J Am Chem Soc (2009) 1.38
Identification and characterization of catabolic para-nitrophenol 4-monooxygenase and para-benzoquinone reductase from Pseudomonas sp. strain WBC-3. J Bacteriol (2009) 1.37
Colorimetric detection of DNA, small molecules, proteins, and ions using unmodified gold nanoparticles and conjugated polyelectrolytes. Proc Natl Acad Sci U S A (2010) 1.27
Generation of highly specific aptamers via micromagnetic selection. Anal Chem (2009) 1.24
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field. J Comput Chem (2009) 1.22
Cerebrospinal fluid concentrations of gefitinib in patients with lung adenocarcinoma. Clin Lung Cancer (2012) 1.21
A ratiometric fluorescent probe based on FRET for imaging Hg2+ ions in living cells. Angew Chem Int Ed Engl (2008) 1.21
Chinese guidelines for the secondary prevention of ischemic stroke and transient ischemic attack 2010. CNS Neurosci Ther (2012) 1.20
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins (2013) 1.20
"Alive" dyes as fluorescent sensors: fluorophore, mechanism, receptor and images in living cells. Chem Commun (Camb) (2010) 1.19
Increased arylhydrocarbon receptor expression offers a potential therapeutic target for pancreatic cancer. Oncogene (2002) 1.15
Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS One (2011) 1.14
Piwil2 expressed in various stages of cervical neoplasia is a potential complementary marker for p16. Am J Transl Res (2010) 1.13
TSC1/2 signaling complex is essential for peripheral naïve CD8+ T cell survival and homeostasis in mice. PLoS One (2012) 1.12
Automated and fast building of three-dimensional RNA structures. Sci Rep (2012) 1.10
Genetic analysis of H1N1 influenza virus from throat swab samples in a microfluidic system for point-of-care diagnostics. J Am Chem Soc (2011) 1.09
Phase I trial of icotinib, a novel epidermal growth factor receptor tyrosine kinase inhibitor, in Chinese patients with non-small cell lung cancer. Chin Med J (Engl) (2011) 1.07
Optimization of a reusable, DNA pseudoknot-based electrochemical sensor for sequence-specific DNA detection in blood serum. Anal Chem (2009) 1.03
ERalpha suppresses slug expression directly by transcriptional repression. Biochem J (2008) 1.03
Derivation and validation of a prediction rule for estimating advanced colorectal neoplasm risk in average-risk Chinese. Am J Epidemiol (2012) 1.02
Process-based network decomposition reveals backbone motif structure. Proc Natl Acad Sci U S A (2010) 1.01
In vitro selection of structure-switching, self-reporting aptamers. Proc Natl Acad Sci U S A (2010) 0.99
Amplified chemiluminescence surface detection of DNA and telomerase activity using catalytic nucleic acid labels. Anal Chem (2004) 0.98
Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis. Biotechnol Bioeng (2014) 0.97
Selection of phage-displayed peptides on live adherent cells in microfluidic channels. Proc Natl Acad Sci U S A (2011) 0.97
Characterization of a para-nitrophenol catabolic cluster in Pseudomonas sp. strain NyZ402 and construction of an engineered strain capable of simultaneously mineralizing both para- and ortho-nitrophenols. Biodegradation (2010) 0.97
Sensitive and selective amplified fluorescence DNA detection based on exonuclease III-aided target recycling. J Am Chem Soc (2010) 0.96
Detection of proteins in serum by micromagnetic aptamer PCR (MAP) technology. Angew Chem Int Ed Engl (2010) 0.96
Metabolic engineering of Synechocystis sp. strain PCC 6803 for isobutanol production. Appl Environ Microbiol (2012) 0.96
An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices. J Am Chem Soc (2010) 0.96
Isomeric boron-fluorine complexes with donor-acceptor architecture: strong solid/liquid fluorescence and large Stokes shift. Org Lett (2008) 0.95
[A multicentre retrospective study of pulmonary mycosis clinically proven from 1998 to 2007]. Zhonghua Jie He He Hu Xi Za Zhi (2011) 0.95
Activatable rotor for quantifying lysosomal viscosity in living cells. J Am Chem Soc (2013) 0.95
Ratiometric and selective fluorescent sensor for CuII based on internal charge transfer (ICT). Org Lett (2005) 0.94
A novel protocol for three-dimensional structure prediction of RNA-protein complexes. Sci Rep (2013) 0.93
RNA stability under different combinations of amber force fields and solvation models. J Biomol Struct Dyn (2010) 0.92
Inhibition of expression of the chromatin remodeling gene, SNF2L, selectively leads to DNA damage, growth inhibition, and cancer cell death. Mol Cancer Res (2009) 0.91
Characterization of gene mutations and phenotypes of cystic fibrosis in Chinese patients. Respirology (2015) 0.91
Concomitant targeting of tumor cells and induction of T-cell response synergizes to effectively inhibit trastuzumab-resistant breast cancer. Cancer Res (2012) 0.90
ASPDock: protein-protein docking algorithm using atomic solvation parameters model. BMC Bioinformatics (2011) 0.90
Long-wavelength, photostable, two-photon excitable BODIPY fluorophores readily modifiable for molecular probes. J Org Chem (2013) 0.89
A lysosome-targetable and two-photon fluorescent probe for monitoring endogenous and exogenous nitric oxide in living cells. J Am Chem Soc (2012) 0.89
A new prodrug-derived ratiometric fluorescent probe for hypoxia: high selectivity of nitroreductase and imaging in tumor cell. Org Lett (2011) 0.88
Clinical outcome of neoadjuvant chemoradiation therapy with oxaliplatin and capecitabine or 5-fluorouracil for locally advanced rectal cancer. J Surg Oncol (2013) 0.88
On the binding of cationic, water-soluble conjugated polymers to DNA: electrostatic and hydrophobic interactions. J Am Chem Soc (2010) 0.87
Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator. ACS Synth Biol (2014) 0.87
Targeting activation-induced cytidine deaminase overcomes tumor evasion of immunotherapy by CTLs. J Immunol (2010) 0.87
Breast carcinomatous tumoral emboli can result from encircling lymphovasculogenesis rather than lymphovascular invasion. Oncotarget (2010) 0.87
Tumor gene mutations and messenger RNA expression: correlation with clinical response to icotinib hydrochloride in non-small cell lung cancer. Chin Med J (Engl) (2011) 0.87
Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution. Nucleic Acids Res (2012) 0.87
[An investigation of the relationship between Lepr gene Gln223Arg polymorphism and obstructive sleep apnea hypopnea syndrome]. Zhonghua Jie He He Hu Xi Za Zhi (2003) 0.87
The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. J Chem Phys (2011) 0.87
i-Motif quadruplex DNA-based biosensor for distinguishing single- and multiwalled carbon nanotubes. J Am Chem Soc (2009) 0.86
Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain. J Mol Biol (2012) 0.86
A phase II study of neoadjuvant chemoradiotherapy with oxaliplatin and capecitabine for rectal cancer. Cancer Lett (2011) 0.86
Disruption of TSC1/2 signaling complex reveals a checkpoint governing thymic CD4+ CD25+ Foxp3+ regulatory T-cell development in mice. FASEB J (2013) 0.86
Human cytochrome P450 4F11: heterologous expression in bacteria, purification, and characterization of catalytic function. Arch Biochem Biophys (2009) 0.85
Inhibition of the acetycholine esterase-stimulated growth of Au nanoparticles: nanotechnology-based sensing of nerve gases. Nano Lett (2005) 0.85
Measurement of aptamer-protein interactions with back-scattering interferometry. Anal Chem (2011) 0.85
Improvements of the hierarchical approach for predicting RNA tertiary structure. J Biomol Struct Dyn (2011) 0.85
A photostable near-infrared fluorescent tracker with pH-independent specificity to lysosomes for long time and multicolor imaging. ACS Appl Mater Interfaces (2014) 0.84
CT-guided percutaneous ethanol injection with disposable curved needle for treatment of malignant liver neoplasms and their metastases in retroperitoneal lymph nodes. World J Gastroenterol (2004) 0.84
Role of ligand binding in structural organization of add A-riboswitch aptamer: a molecular dynamics simulation. J Biomol Struct Dyn (2011) 0.84
Optical and electrochemical detection of NADH and of NAD+-dependent biocatalyzed processes by the catalytic deposition of copper on gold nanoparticles. Small (2005) 0.84
Computational methods to predict long noncoding RNA functions based on co-expression network. Methods Mol Biol (2014) 0.84
Synthesis and evaluation of novel 8-oxo-8H-cyclopenta[a]acenaphthylene-7-carbonitriles as long-wavelength fluorescent markers for hypoxic cells in solid tumor. Bioorg Med Chem Lett (2006) 0.83
Reversal of multi-drug resistance by pSUPER-shRNA-mdr1 in vivo and in vitro. World J Gastroenterol (2009) 0.83
Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. J Am Chem Soc (2010) 0.83
A label-free aptamer-fluorophore assembly for rapid and specific detection of cocaine in biofluids. Anal Chem (2014) 0.82
A simple method of identifying symmetric substructures of proteins. Comput Biol Chem (2008) 0.82
Evaluation of peripheral artery stent with 64-slice multi-detector row CT angiography: prospective comparison with digital subtraction angiography. Eur J Radiol (2009) 0.82
Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. Anal Chem (2011) 0.82
Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae. Microb Cell Fact (2011) 0.82
Characterization of catabolic meta-nitrophenol nitroreductase from Cupriavidus necator JMP134. Appl Microbiol Biotechnol (2010) 0.82
A design concept of long-wavelength fluorescent analogs of rhodamine dyes: replacement of oxygen with silicon atom. Chem Commun (Camb) (2008) 0.81
Versatile nitro-fluorophore as highly effective sensor for hypoxic tumor cells: design, imaging and evaluation. J Fluoresc (2008) 0.81
Epitope-vaccine strategy against HIV-1: today and tomorrow. Immunobiology (2003) 0.81
Prognostic Role of Neutrophil-to-Lymphocyte Ratio in Prostate Cancer: A Systematic Review and Meta-analysis. Medicine (Baltimore) (2016) 0.81
A method for identification of selenoprotein genes in archaeal genomes. Genomics Proteomics Bioinformatics (2009) 0.81
Signal therapy of human pancreatic cancer and NF1-deficient breast cancer xenograft in mice by a combination of PP1 and GL-2003, anti-PAK1 drugs (Tyr-kinase inhibitors). Cancer Lett (2006) 0.81
Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins. J Comput Chem (2010) 0.81
Amplified single base-pair mismatch detection via aggregation of exonuclease-sheared gold nanoparticles. Anal Chem (2014) 0.80
Identification of differentially expressed genes between cloned and zygote-developing zebrafish (Danio rerio) embryos at the dome stage using suppression subtractive hybridization. Biol Reprod (2008) 0.80
A directed essential dynamics simulation of peptide folding. Biophys J (2005) 0.80
A common sequence-associated physicochemical feature for proteins of beta-trefoil family. Comput Biol Chem (2005) 0.80
A prediction rule for estimating pancreatic cancer risk in chronic pancreatitis patients with focal pancreatic mass lesions with prior negative EUS-FNA cytology. Scand J Gastroenterol (2010) 0.80
2,3,6,7-Tetraamino-9,9-bis(2-ethylhexyl)fluorene: new multifunctional monomer for soluble ladder-conjugated molecules and polymers. Org Lett (2008) 0.80
Human leukocyte antigen (HLA) typing by DNA sequencing. Methods Mol Biol (2013) 0.80
Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories. Bioinformatics (2008) 0.80
Continuous positive airway pressure is associated with a decrease in pulmonary artery pressure in patients with obstructive sleep apnoea: a meta-analysis. Respirology (2014) 0.80
Identification and fine mapping of AvrPi15, a novel avirulence gene of Magnaporthe grisea. Theor Appl Genet (2006) 0.79