A structural perspective on protein-protein interactions.

Protein structure fitting and refinement guided by cryo-EM density. Structure (2008) 3.12

Protein binding site prediction using an empirical scoring function. Nucleic Acids Res (2006) 2.19

NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85

Subunit architecture of multimeric complexes isolated directly from cells. EMBO Rep (2006) 1.75

Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics (2009) 1.38

Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected. Proc Natl Acad Sci U S A (2010) 1.34

Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (2011) 1.34

Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol (2011) 1.30

Oligomeric protein structure networks: insights into protein-protein interactions. BMC Bioinformatics (2005) 1.27

Computational methods for biomolecular electrostatics. Methods Cell Biol (2008) 1.27

Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol (2006) 1.27

Templates are available to model nearly all complexes of structurally characterized proteins. Proc Natl Acad Sci U S A (2012) 1.26

Docking by structural similarity at protein-protein interfaces. Proteins (2010) 1.26

VASCo: computation and visualization of annotated protein surface contacts. BMC Bioinformatics (2009) 1.22

SSMap: a new UniProt-PDB mapping resource for the curation of structural-related information in the UniProt/Swiss-Prot Knowledgebase. BMC Bioinformatics (2008) 1.18

iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics (2010) 1.17

Future directions of structural mass spectrometry using hydroxyl radical footprinting. J Mass Spectrom (2010) 1.16

Reporter gene imaging of protein-protein interactions in living subjects. Curr Opin Biotechnol (2007) 1.11

M-TASSER: an algorithm for protein quaternary structure prediction. Biophys J (2007) 1.08

Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Comput Biol (2006) 1.07

High-resolution structure determination of the CylR2 homodimer using paramagnetic relaxation enhancement and structure-based prediction of molecular alignment. J Biomol NMR (2007) 1.06

Analysis of self-associating proteins by singular value decomposition of solution scattering data. Biophys J (2008) 1.05

Protein-protein docking: from interaction to interactome. Biophys J (2014) 1.05

Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics (2012) 1.00

New benchmark metrics for protein-protein docking methods. Proteins (2011) 0.97

Accuracy of protein-protein binding sites in high-throughput template-based modeling. PLoS Comput Biol (2010) 0.97

A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints. J Biomol NMR (2006) 0.96

Functional organization of the yeast proteome by a yeast interactome map. Proc Natl Acad Sci U S A (2009) 0.95

Global and local structural similarity in protein-protein complexes: implications for template-based docking. Proteins (2013) 0.94

Optimization of electrostatic interactions in protein-protein complexes. Biophys J (2007) 0.94

Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks. Bioinformatics (2009) 0.91

Mapping of protein-protein interaction sites by the 'absence of interference' approach. J Mol Biol (2007) 0.90

GWIDD: Genome-wide protein docking database. Nucleic Acids Res (2009) 0.90

Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures. Protein Sci (2008) 0.89

Parameter estimate of signal transduction pathways. BMC Neurosci (2006) 0.89

Protein docking by the interface structure similarity: how much structure is needed? PLoS One (2012) 0.87

Prediction of protein-binding areas by small-world residue networks and application to docking. BMC Bioinformatics (2011) 0.86

Testis-expressed profilins 3 and 4 show distinct functional characteristics and localize in the acroplaxome-manchette complex in spermatids. BMC Cell Biol (2009) 0.85

Toward a three-dimensional view of protein networks between species. Front Microbiol (2012) 0.85

Antibody-array interaction mapping, a new method to detect protein complexes applied to the discovery and study of serum amyloid P interactions with kininogen in human plasma. Mol Cell Proteomics (2009) 0.84

Structural deformation upon protein-protein interaction: a structural alphabet approach. BMC Struct Biol (2008) 0.83

Tools used to study how protein complexes are assembled in signaling cascades. Bioeng Bugs (2011) 0.83

Computational methods for predicting sites of functionally important dynamics. J Phys Chem B (2009) 0.82

Computational study of the heterodimerization between mu and delta receptors. J Comput Aided Mol Des (2009) 0.81

REACH coarse-grained normal mode analysis of protein dimer interaction dynamics. Biophys J (2009) 0.81

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network. Nucleic Acids Res (2014) 0.80

Protein-protein interactions as a strategy towards protein-specific drug design: the example of ataxin-1. PLoS One (2013) 0.79

SPPS: a sequence-based method for predicting probability of protein-protein interaction partners. PLoS One (2012) 0.78

GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions. Hum Genomics (2012) 0.78

Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes. Biochemistry (2011) 0.78

Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors. J Comput Aided Mol Des (2006) 0.78

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction. Adv Appl Bioinform Chem (2009) 0.77

A contact energy function considering residue hydrophobic environment and its application in protein fold recognition. Genomics Proteomics Bioinformatics (2005) 0.77

Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution. Comput Struct Biotechnol J (2015) 0.76

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking. Sci Rep (2016) 0.75

Decomposing the space of protein quaternary structures with the interface fragment pair library. BMC Bioinformatics (2015) 0.75

Protein social behavior makes a stronger signal for partner identification than surface geometry. Proteins (2016) 0.75

Computational study for protein-protein docking using global optimization and empirical potentials. Int J Mol Sci (2008) 0.75

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. Database (Oxford) (2016) 0.75

Novel octavalent cross-linker displays efficient trapping of protein-protein interactions. Chem Commun (Camb) (2007) 0.75

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 8.98

Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol (2003) 7.15

The molecular architecture of the nuclear pore complex. Nature (2007) 6.93

Protein structure modeling with MODELLER. Methods Mol Biol (2008) 6.28

Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci (2007) 5.81

Determining the architectures of macromolecular assemblies. Nature (2007) 4.94

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol (2011) 4.56

MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2004) 4.54

Outcome of the first electron microscopy validation task force meeting. Structure (2012) 4.35

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell (2008) 4.00

Protein production and purification. Nat Methods (2008) 3.97

FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res (2010) 3.91

Global landscape of HIV-human protein complexes. Nature (2011) 3.70

Tools for comparative protein structure modeling and analysis. Nucleic Acids Res (2003) 3.68

MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2006) 3.56

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A (2012) 3.42

ModLoop: automated modeling of loops in protein structures. Bioinformatics (2003) 3.31

The molecular sociology of the cell. Nature (2007) 3.23

Protein structure fitting and refinement guided by cryo-EM density. Structure (2008) 3.12

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics (2005) 3.05

Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Cell (2003) 3.03

Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure (2008) 2.98

ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res (2010) 2.96

Statistical potentials for fold assessment. Protein Sci (2002) 2.92

Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol (2004) 2.90

Alignment of protein sequences by their profiles. Protein Sci (2004) 2.80

Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature (2011) 2.71

Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov (2008) 2.58

EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res (2003) 2.50

Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res (2003) 2.44

PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics (2005) 2.39

Reliability of assessment of protein structure prediction methods. Structure (2002) 2.39

Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol (2012) 2.37

Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A (2006) 2.35

Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem (2008) 2.35

A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics (2011) 2.34

Outcome of a workshop on archiving structural models of biological macromolecules. Structure (2006) 2.32

Potential artefacts in protein-interaction networks. FEBS Lett (2002) 2.24

3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res (2005) 2.18

Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2014) 2.17

The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol (2005) 2.13

Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure (2008) 2.11

Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol (2011) 2.10

UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol (2011) 2.10

Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol (2006) 2.06

Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci (2010) 2.06

Outcome of a workshop on applications of protein models in biomedical research. Structure (2009) 2.05

Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol (2008) 2.05

Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics (2012) 2.03

MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res (2008) 2.02

MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res (2002) 2.01

ModView, visualization of multiple protein sequences and structures. Bioinformatics (2003) 1.99

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res (2012) 1.95

A composite score for predicting errors in protein structure models. Protein Sci (2006) 1.92

Structural genomics: a pipeline for providing structures for the biologist. Protein Sci (2002) 1.91

Interactome3D: adding structural details to protein networks. Nat Methods (2012) 1.89

Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res (2007) 1.89

The Enzyme Function Initiative. Biochemistry (2011) 1.87

Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res (2004) 1.84

A network medicine approach to human disease. FEBS Lett (2009) 1.83

Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J (2013) 1.83

Insights into the molecular architecture of the 26S proteasome. Proc Natl Acad Sci U S A (2009) 1.81

Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol Cell Proteomics (2009) 1.74

3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res (2010) 1.71

Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A (2008) 1.68

Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol (2005) 1.67

Protein structure modeling with MODELLER. Methods Mol Biol (2014) 1.65

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics (2002) 1.62

Crystal structure of a eukaryotic phosphate transporter. Nature (2013) 1.60

Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology (2006) 1.58

The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together. Proc Natl Acad Sci U S A (2011) 1.57

High-throughput computational and experimental techniques in structural genomics. Genome Res (2004) 1.55

How well can the accuracy of comparative protein structure models be predicted? Protein Sci (2008) 1.52

Biochemistry. Integrative structural biology. Science (2013) 1.52

3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res (2008) 1.51

Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol (2008) 1.51

A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation. Nat Struct Mol Biol (2008) 1.50

The genetics of hyperekplexia: more than startle! Trends Genet (2008) 1.49

Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol (2006) 1.49

Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics (2010) 1.48

Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol (2009) 1.48

Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J Biol Chem (2010) 1.44

Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol (2012) 1.44

Protein complexes: structure prediction challenges for the 21st century. Curr Opin Struct Biol (2005) 1.43

Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia (2007) 1.43

Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel (2009) 1.43

A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature (2012) 1.42

Structure of an apoptosome-procaspase-9 CARD complex. Structure (2010) 1.42