Published in Proteins on July 01, 2003
PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66
GRAMM-X public web server for protein-protein docking. Nucleic Acids Res (2006) 3.71
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci U S A (2005) 2.84
Protein-protein docking benchmark version 4.0. Proteins (2010) 2.78
Improved side-chain modeling for protein-protein docking. Protein Sci (2005) 2.72
Protein-protein docking benchmark version 3.0. Proteins (2008) 2.54
FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res (2008) 2.39
Protein binding site prediction using an empirical scoring function. Nucleic Acids Res (2006) 2.19
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res (2010) 2.05
Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol (2008) 2.03
A structure-based benchmark for protein-protein binding affinity. Protein Sci (2011) 1.81
How good is automated protein docking? Proteins (2013) 1.80
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol (2007) 1.74
The many faces of protein-protein interactions: A compendium of interface geometry. PLoS Comput Biol (2006) 1.71
Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res (2006) 1.70
Optimal clustering for detecting near-native conformations in protein docking. Biophys J (2005) 1.59
DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J (2008) 1.50
Assessing predictions of protein-protein interaction: the CAPRI experiment. Protein Sci (2005) 1.48
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics (2009) 1.38
Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol (2008) 1.36
Discrimination of near-native structures in protein-protein docking by testing the stability of local minima. Proteins (2008) 1.27
Docking by structural similarity at protein-protein interfaces. Proteins (2010) 1.26
Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res (2005) 1.11
Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking. Proc Natl Acad Sci U S A (2008) 1.05
A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins (2007) 1.05
Sampling and scoring: a marriage made in heaven. Proteins (2013) 1.02
A Protein Classification Benchmark collection for machine learning. Nucleic Acids Res (2006) 1.01
SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci (2010) 1.01
Multi-LZerD: multiple protein docking for asymmetric complexes. Proteins (2012) 1.00
Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys J (2007) 0.97
A nonredundant structure dataset for benchmarking protein-RNA computational docking. J Comput Chem (2012) 0.95
A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Res (2014) 0.95
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol (2015) 0.95
Optimization of electrostatic interactions in protein-protein complexes. Biophys J (2007) 0.94
In silico modeling of pH-optimum of protein-protein binding. Proteins (2010) 0.93
A collaborative filtering approach for protein-protein docking scoring functions. PLoS One (2011) 0.93
Rice mitogen activated protein kinase kinase and mitogen activated protein kinase interaction network revealed by in-silico docking and yeast two-hybrid approaches. PLoS One (2013) 0.91
Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization. Protein Sci (2007) 0.91
Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Sci (2005) 0.90
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins (2010) 0.88
DOT2: Macromolecular docking with improved biophysical models. J Comput Chem (2013) 0.86
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams. BMC Bioinformatics (2011) 0.86
Crystal structural analysis of protein-protein interactions drastically destabilized by a single mutation. Protein Sci (2008) 0.86
Encounter complexes and dimensionality reduction in protein-protein association. Elife (2014) 0.84
Association of putative concave protein-binding sites with the fluctuation behavior of residues. Protein Sci (2006) 0.84
Benchmarks for flexible and rigid transcription factor-DNA docking. BMC Struct Biol (2011) 0.82
Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem. Protein Sci (2003) 0.82
Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro. J Comput Chem (2015) 0.81
Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol (2015) 0.81
Scoring function based on weighted residue network. Int J Mol Sci (2011) 0.80
The impact of side-chain packing on protein docking refinement. J Chem Inf Model (2015) 0.80
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking. Protein Sci (2011) 0.80
Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins. BMC Struct Biol (2012) 0.79
The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners. Proteins (2010) 0.79
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. Conf Proc IEEE Eng Med Biol Soc (2006) 0.78
The ClusPro web server for protein-protein docking. Nat Protoc (2017) 0.77
Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol (2015) 0.77
Automatic prediction of flexible regions improves the accuracy of protein-protein docking models. J Mol Model (2011) 0.77
Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints. PLoS One (2013) 0.77
Focused grid-based resampling for protein docking and mapping. J Comput Chem (2016) 0.77
Computer applications for prediction of protein-protein interactions and rational drug design. Adv Appl Bioinform Chem (2009) 0.77
CIRSE: a solvation energy estimator compatible with flexible protein docking and design applications. Protein Sci (2006) 0.76
An avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin. Protein Sci (2005) 0.75
Receptor modification as a therapeutic approach against viral diseases. Bioinformation (2012) 0.75
New Additions to the ClusPro Server Motivated by CAPRI. Proteins (2016) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet (2007) 32.41
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science (2008) 8.62
ZDOCK: an initial-stage protein-docking algorithm. Proteins (2003) 7.52
Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res (2004) 6.31
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet (2007) 5.93
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A (2006) 5.27
Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell (2010) 5.22
Nucleosome positioning signals in genomic DNA. Genome Res (2007) 4.99
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet (2008) 4.91
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods (2012) 4.89
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
Dissecting protein-protein recognition sites. Proteins (2002) 4.51
Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell (2009) 4.39
Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Science (2008) 4.15
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res (2003) 3.99
Target RNA-directed trimming and tailing of small silencing RNAs. Science (2010) 3.98
A dissection of specific and non-specific protein-protein interfaces. J Mol Biol (2004) 3.77
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Predictome: a database of putative functional links between proteins. Nucleic Acids Res (2002) 3.32
A protein complex network of Drosophila melanogaster. Cell (2011) 3.31
Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA (2009) 3.19
Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell (2011) 3.19
The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell (2009) 3.13
Protein-Protein Docking Benchmark 2.0: an update. Proteins (2005) 3.13
Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins (2002) 2.95
ZRANK: reranking protein docking predictions with an optimized energy function. Proteins (2007) 2.79
Protein-protein docking benchmark version 4.0. Proteins (2010) 2.78
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A (2005) 2.69
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res (2010) 2.56
Protein-protein docking benchmark version 3.0. Proteins (2008) 2.54
Integrating statistical pair potentials into protein complex prediction. Proteins (2007) 2.53
Transcription factor binding and modified histones in human bidirectional promoters. Genome Res (2007) 2.40
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci (2004) 2.38
Finding functional sequence elements by multiple local alignment. Nucleic Acids Res (2004) 2.37
Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res (2008) 2.33
Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS One (2011) 2.33
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res (2012) 2.32
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res (2002) 2.30
FAST: a novel protein structure alignment algorithm. Proteins (2005) 2.27
Dissecting subunit interfaces in homodimeric proteins. Proteins (2003) 2.24
RDOCK: refinement of rigid-body protein docking predictions. Proteins (2003) 2.24
An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell (2013) 2.23
Unexpected role of interferon-γ in regulating neuronal connectivity and social behaviour. Nature (2016) 2.21
Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol (2010) 2.15
CisML: an XML-based format for sequence motif detection software. Bioinformatics (2004) 2.13
Functional analysis of transcription factor binding sites in human promoters. Genome Biol (2012) 2.12
Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A (2010) 2.06
A novel shape complementarity scoring function for protein-protein docking. Proteins (2003) 2.03
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res (2007) 2.03
Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods (2008) 2.02
The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell (2012) 1.88
The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins (2007) 1.85
Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res (2004) 1.84
Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res (2007) 1.82
Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res (2007) 1.81
Epigenetic signatures of autism: trimethylated H3K4 landscapes in prefrontal neurons. Arch Gen Psychiatry (2011) 1.81
A structure-based benchmark for protein-protein binding affinity. Protein Sci (2011) 1.81
Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains. Mol Cell (2011) 1.79
Adaptation to P element transposon invasion in Drosophila melanogaster. Cell (2011) 1.76
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics (2003) 1.71
PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res (2003) 1.68
Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods (2012) 1.67
Dissecting protein-RNA recognition sites. Nucleic Acids Res (2008) 1.67
The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1. Curr Biol (2011) 1.66
Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis [corrected] . PLoS One (2010) 1.65
Ancestral and consensus envelope immunogens for HIV-1 subtype C. Virology (2006) 1.62
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins (2005) 1.61
Structural basis of macromolecular recognition. Adv Protein Chem (2002) 1.60
Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett (2010) 1.58
Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell (2012) 1.57
UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell (2012) 1.53
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res (2004) 1.52
HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Res (2002) 1.52
Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins. Virology (2006) 1.51
Atomic contact vectors in protein-protein recognition. Proteins (2003) 1.48
A combination of rescoring and refinement significantly improves protein docking performance. Proteins (2008) 1.48
Hydration of protein-protein interfaces. Proteins (2005) 1.47
PromoSer: improvements to the algorithm, visualization and accessibility. Nucleic Acids Res (2004) 1.45
M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics (2004) 1.43
Sequence features that drive human promoter function and tissue specificity. Genome Res (2010) 1.40
A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res (2002) 1.40
Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol (2011) 1.40
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins (2010) 1.39