Published in Proteins on September 01, 2002
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res (2004) 5.19
Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol (2005) 3.88
Nicotinic receptors: allosteric transitions and therapeutic targets in the nervous system. Nat Rev Drug Discov (2009) 3.26
Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys J (2005) 2.33
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc Natl Acad Sci U S A (2006) 2.23
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res (2006) 2.21
On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc Natl Acad Sci U S A (2004) 2.09
The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res (2006) 1.89
MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res (2003) 1.87
How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys J (2007) 1.79
Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A (2009) 1.76
Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure (2008) 1.76
Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins (2008) 1.68
iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics (2005) 1.65
The role of shape in determining molecular motions. Biophys J (2005) 1.53
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci U S A (2008) 1.51
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci (2005) 1.51
Molecular crowding inhibits intramolecular breathing motions in proteins. J Mol Biol (2007) 1.46
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. Acta Crystallogr D Biol Crystallogr (2007) 1.40
Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy. Proc Natl Acad Sci U S A (2005) 1.34
An analysis of core deformations in protein superfamilies. Biophys J (2004) 1.33
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res (2007) 1.32
Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J (2007) 1.31
Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages. Genome Biol (2007) 1.20
Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Struct Biol (2007) 1.14
The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261. Biochemistry (2006) 1.14
Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys J (2005) 1.14
Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res (2005) 1.11
Tightening of the ATP-binding sites induces the opening of P2X receptor channels. EMBO J (2012) 1.11
Modeling activated states of GPCRs: the rhodopsin template. J Comput Aided Mol Des (2006) 1.06
Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinformatics (2007) 1.06
The dynamic stator stalk of rotary ATPases. Nat Commun (2012) 1.06
SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci (2010) 1.01
On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm. PLoS Comput Biol (2010) 1.01
Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit. J Chem Phys (2008) 1.00
Flexibility in a drug transport accessory protein: molecular dynamics simulations of MexA. Biophys J (2006) 1.00
MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Res (2004) 0.96
Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Res (2005) 0.93
Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members. PLoS Comput Biol (2011) 0.93
Iterative cluster-NMA: A tool for generating conformational transitions in proteins. Proteins (2009) 0.93
Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis. Biophys J (2009) 0.91
Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol (2014) 0.91
Inhibition mechanism of the acetylcholine receptor by alpha-neurotoxins as revealed by normal-mode dynamics. Biochemistry (2008) 0.90
Alzheimer's abeta(1-40) amyloid fibrils feature size-dependent mechanical properties. Biophys J (2010) 0.90
Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Biophys J (2009) 0.90
Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach. Biophys J (2008) 0.90
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. BMC Struct Biol (2009) 0.89
Structure-based protein NMR assignments using native structural ensembles. J Biomol NMR (2008) 0.89
WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics (2014) 0.88
A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure. Acta Crystallogr D Biol Crystallogr (2006) 0.88
Computational methods for constructing protein structure models from 3D electron microscopy maps. J Struct Biol (2013) 0.87
ΔΔPT: a comprehensive toolbox for the analysis of protein motion. BMC Bioinformatics (2013) 0.85
Characterizing protein motions from structure. J Mol Graph Model (2011) 0.84
Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures. Biophys J (2010) 0.83
Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis. Proteins (2008) 0.82
Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition. PLoS One (2012) 0.81
Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Curr Protein Pept Sci (2009) 0.81
Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes. Biophys J (2011) 0.81
Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures. Protein Sci (2011) 0.80
iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res (2015) 0.80
Normal modes of prion proteins: from native to infectious particle. Biochemistry (2011) 0.80
Predicting protein ligand binding motions with the conformation explorer. BMC Bioinformatics (2011) 0.80
Features of large hinge-bending conformational transitions. Prediction of closed structure from open state. Biophys J (2014) 0.79
Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid. Biophys J (2012) 0.79
A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation. J Gen Physiol (2015) 0.79
A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations. PLoS One (2015) 0.78
SCEDS: protein fragments for molecular replacement in Phaser. Acta Crystallogr D Biol Crystallogr (2013) 0.78
PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment. J Mol Biol (2013) 0.77
Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics. J Phys Chem B (2014) 0.77
ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution. J Chem Theory Comput (2016) 0.76
Flexibility of the exportins Cse1p and Xpot depicted by elastic network model. J Mol Model (2010) 0.76
Characterization and Prediction of Protein Flexibility Based on Structural Alphabets. Biomed Res Int (2016) 0.75
Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein. Sci Rep (2016) 0.75
Vinculin motion modes analysis with elastic network model. Int J Mol Sci (2011) 0.75
The flexibility and dynamics of protein disulfide isomerase. Proteins (2016) 0.75
Elastic network model of learned maintained contacts to predict protein motion. PLoS One (2017) 0.75
Normal mode dynamics of voltage-gated K(+) channels: gating principle, opening mechanism, and inhibition. J Comput Neurosci (2014) 0.75
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature (2006) 24.29
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
A map of the interactome network of the metazoan C. elegans. Science (2004) 15.60
Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell (2012) 12.32
A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science (2003) 12.07
Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr (2012) 11.31
Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Subcellular localization of the yeast proteome. Genes Dev (2002) 7.93
Global analysis of protein phosphorylation in yeast. Nature (2005) 7.46
Divergence of transcription factor binding sites across related yeast species. Science (2007) 7.10
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res (2011) 6.97
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
An empirical framework for binary interactome mapping. Nat Methods (2008) 6.59
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev (2005) 6.14
Relating whole-genome expression data with protein-protein interactions. Genome Res (2002) 5.78
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res (2003) 5.49
An experimentally derived confidence score for binary protein-protein interactions. Nat Methods (2008) 5.27
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
A cis-regulatory map of the Drosophila genome. Nature (2011) 4.80
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev (2007) 4.62
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Literature-curated protein interaction datasets. Nat Methods (2009) 4.21
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res (2008) 4.08
Edgetic perturbation models of human inherited disorders. Mol Syst Biol (2009) 3.96
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
An integrated approach for finding overlooked genes in yeast. Nat Biotechnol (2002) 3.88
The Phenix software for automated determination of macromolecular structures. Methods (2011) 3.81
Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods (2012) 3.69
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res (2006) 3.62
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol (2012) 3.61
Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science (2013) 3.60
Genomic analysis of essentiality within protein networks. Trends Genet (2004) 3.52
Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51
Modeling ChIP sequencing in silico with applications. PLoS Comput Biol (2008) 3.48
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Structured digital abstract makes text mining easy. Nature (2007) 3.38
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A (2010) 3.28
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22
The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A (2012) 3.12
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature (2012) 3.09
Getting connected: analysis and principles of biological networks. Genes Dev (2007) 3.03
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell (2007) 2.95
Accessing protein conformational ensembles using room-temperature X-ray crystallography. Proc Natl Acad Sci U S A (2011) 2.92
Analyzing protein function on a genomic scale: the importance of gold-standard positives and negatives for network prediction. Curr Opin Microbiol (2004) 2.92
Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
PubNet: a flexible system for visualizing literature derived networks. Genome Biol (2005) 2.89
Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability. Nucleic Acids Res (2005) 2.89
Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res (2002) 2.88
PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics (2006) 2.85
Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res (2003) 2.85
Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A (2009) 2.83
The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev Cell (2005) 2.81
Modeling gene expression using chromatin features in various cellular contexts. Genome Biol (2012) 2.76
Genomics. Defining genes in the genomics era. Science (2003) 2.73
Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotechnol (2012) 2.67
MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev (2008) 2.66
DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A (2004) 2.66
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 2.66
Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell (2004) 2.65
Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet (2002) 2.65
Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol (2005) 2.54
Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet (2004) 2.51
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods (2009) 2.50
Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol (2007) 2.48
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet (2010) 2.46
Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proc Natl Acad Sci U S A (2012) 2.43
TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell (2006) 2.42
Target hub proteins serve as master regulators of development in yeast. Genes Dev (2006) 2.39
Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev (2004) 2.38
Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38
Personal genome sequencing: current approaches and challenges. Genes Dev (2010) 2.38
Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol (2004) 2.37
Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet (2005) 2.36