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==Citation Data==
==Citation Data==
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This page provides data on how frequently MolMovDB-related work by the Gerstein lab has been cited in the literature. Note that it was last updated in June 2011.
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This page provides data on how frequently MolMovDB-related work by the Gerstein lab has been cited in the literature. Note that it was last updated in Jan 2012.
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!Paper Title & Link!!Year Published!!class="unsortable"|No. Times Cited (as of 6/2011)
!Paper Title & Link!!Year Published!!class="unsortable"|No. Times Cited (as of 6/2011)
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/3v/index.html '''3V: cavity, channel and cleft volume calculator and extractor''']||style="width:15%; text-align:center;"|2010||style="text-align:center;"|2
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|style="width:65%"|[http://papers.gersteinlab.org/papers/dynasin/index.html '''Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions''']||style="width:15%; text-align:center;"|2011||style="text-align:center;"|1
|-style="height: 50px;"
|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/rigidfinder/index.html '''RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes''']||style="width:15%; text-align:center;"|2010||style="text-align:center;"|1
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|style="width:65%"|[http://papers.gersteinlab.org/papers/3v/index.html '''3V: cavity, channel and cleft volume calculator and extractor''']||style="width:15%; text-align:center;"|2010||style="text-align:center;"|9
|-style="height: 50px;"
|-style="height: 50px;"
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|style="width:65%"|[http://archive.gersteinlab.org/proj/rnaseq/IQSeq/ '''IQseq''']||style="text-align:center;"|2010||A tool for isoform quantification with RNA-seq data. Given isoform annotation and alignment of RNA-seq reads, it will use an EM algorithm to infer the most probable expression level for each isoform of a gene.
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|style="width:65%"|[http://papers.gersteinlab.org/papers/rigidfinder/index.html '''RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes''']||style="width:15%; text-align:center;"|2010||style="text-align:center;"|2
|-style="height: 50px;"
|-style="height: 50px;"
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|style="width:65%"|[http://archive.gersteinlab.org/proj/rnaseq/rseqtools/ '''RSEQtools''']||style="text-align:center;"|2010||A suite of tools that use Mapped Read Format (MRF) for the analysis of RNA-Seq experiments. MRF was developed to address privacy concerns associated with the potential for mRNA sequence reads to identify and genetically characterise specific individuals; it is a compact data summary format that enables anonymization of confidential sequence information, while maintaining the ability to conduct subsequent functional genomics studies. RSEQtools provides a suite of modules that convert to/from MRF data and perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions.
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|style="width:65%"|[http://papers.gersteinlab.org/papers/packingeff/index.html '''Relating protein conformational changes to packing efficiency and disorder''']||style="width:15%; text-align:center;"|2009||style="text-align:center;"|2
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/stonehinge/index.html '''StoneHinge: hinge prediction by network analysis of individual protein structures''']||style="width:15%; text-align:center;"|2009||style="text-align:center;"|11
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/hingemaster/index.html '''HingeMaster: normal mode hinge prediction approach and integration of complementary predictors''']||style="width:15%; text-align:center;"|2008||style="text-align:center;"|18
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/flexoracle/index.html '''FlexOracle: predicting flexible hinges by identification of stable domains''']||style="width:15%; text-align:center;"|2007||style="text-align:center;"|21
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/HingeAtlas/index.html '''Hinge Atlas: relating protein sequence to sites of structural flexibility''']||style="width:15%; text-align:center;"|2007||style="text-align:center;"|16
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/molmovdb-update-nar/index.html '''The Database of Macromolecular Motions: new features added at the decade mark''']||style="width:15%; text-align:center;"|2006||style="text-align:center;"|93
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/hit/index.html '''Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins''']||style="width:15%; text-align:center;"|2006||style="text-align:center;"|9
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/ribotunnel/index.html '''The geometry of the ribosomal polypeptide exit tunnel''']||style="width:15%; text-align:center;"|2006||style="text-align:center;"|113
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/nmodes2/index.html '''Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool''']||style="width:15%; text-align:center;"|2005||style="text-align:center;"|81
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/nucprot/index.html '''Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly''']||style="width:15%; text-align:center;"|2005||style="text-align:center;"|53
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/protconf-cosb/index.html '''Conformational changes associated with protein-protein interactions''']||style="width:15%; text-align:center;"|2004||style="text-align:center;"|138
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/largemot-cocb/index.html '''Exploring the range of protein flexibility, from a structural proteomics perspective''']||style="width:15%; text-align:center;"|2004||style="text-align:center;"|57
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/3dhmm/index.html '''Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures''']||style="width:15%; text-align:center;"|2004||style="text-align:center;"|31
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/mots-mie/index.html '''Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences''']||style="width:15%; text-align:center;"|2003||style="text-align:center;"|11
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/molmovdb2/index.html '''MolMovDB: analysis and visualization of conformational change and structural flexibility''']||style="width:15%; text-align:center;"|2003||style="text-align:center;"|131
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/nmodes/index.html '''Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic''']||style="width:15%; text-align:center;"|2002||style="text-align:center;"|158
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/vol-sensanal-bioinfo/index.html '''Calculations of protein volumes: sensitivity analysis and parameter database''']||style="width:15%; text-align:center;"|2002||style="text-align:center;"|42
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/min-atomtypes-bioinfo/index.html '''Determining the minimum number of types necessary to represent the sizes of protein atoms''']||style="width:15%; text-align:center;"|2001||style="text-align:center;"|18
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/geom-inttab/index.html '''Protein Geometry: Distances, Areas, and Volumes''']||style="width:15%; text-align:center;"|2001||style="text-align:center;"|10
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/morphs-nar/index.html '''The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework''']||style="width:15%; text-align:center;"|2000||style="text-align:center;"|131
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/std-vols-jmb/index.html '''The packing density in proteins: standard radii and volumes''']||style="width:15%; text-align:center;"|1999||style="text-align:center;"|313
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/protmot-science/index.html '''Perspectives: signal transduction. Proteins in motion''']||style="width:15%; text-align:center;"|1999||style="text-align:center;"|16
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/molmovdb-nar/index.html '''A database of macromolecular motions''']||style="width:15%; text-align:center;"|1998||style="text-align:center;"|246
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/surfpack-pnas/index.html '''Packing at the protein-water interface''']||style="width:15%; text-align:center;"|1996||style="text-align:center;"|159
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/structmovprot/index.html '''Structural mechanisms for domain movements in proteins''']||style="width:15%; text-align:center;"|1994||style="text-align:center;"|578
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|-style="height: 50px;"
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|style="width:65%"|[http://papers.gersteinlab.org/papers/volfold-structure/index.html '''Volume changes on protein folding''']||style="width:15%; text-align:center;"|1994||style="text-align:center;"|346
|}
|}

Current revision

Citation Data

This page provides data on how frequently MolMovDB-related work by the Gerstein lab has been cited in the literature. Note that it was last updated in Jan 2012.


Paper Title & LinkYear PublishedNo. Times Cited (as of 6/2011)
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions20111
3V: cavity, channel and cleft volume calculator and extractor20109
RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes20102
Relating protein conformational changes to packing efficiency and disorder20092
StoneHinge: hinge prediction by network analysis of individual protein structures200911
HingeMaster: normal mode hinge prediction approach and integration of complementary predictors200818
FlexOracle: predicting flexible hinges by identification of stable domains200721
Hinge Atlas: relating protein sequence to sites of structural flexibility200716
The Database of Macromolecular Motions: new features added at the decade mark200693
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins20069
The geometry of the ribosomal polypeptide exit tunnel2006113
Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool200581
Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly200553
Conformational changes associated with protein-protein interactions2004138
Exploring the range of protein flexibility, from a structural proteomics perspective200457
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures200431
Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences200311
MolMovDB: analysis and visualization of conformational change and structural flexibility2003131
Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic2002158
Calculations of protein volumes: sensitivity analysis and parameter database200242
Determining the minimum number of types necessary to represent the sizes of protein atoms200118
Protein Geometry: Distances, Areas, and Volumes200110
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework2000131
The packing density in proteins: standard radii and volumes1999313
Perspectives: signal transduction. Proteins in motion199916
A database of macromolecular motions1998246
Packing at the protein-water interface1996159
Structural mechanisms for domain movements in proteins1994578
Volume changes on protein folding1994346
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