bmc_article.bib

@article{laskowski2011ligplot+,
  title={LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery},
  author={Laskowski, RA and Swindells, MB},
  journal={Journal of chemical information and modeling},
  year={2011}
}


@article{kozlikova2014caver,
  title={CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures},
  author={Kozlikova, Barbora and Sebestova, Eva and Sustr, Vilem and Brezovsky, Jan and Strnad, Ondrej and Daniel, Lukas and Bednar, David and Pavelka, Antonin and Manak, Martin and Bezdeka, Martin and others},
  journal={Bioinformatics},
  volume={30},
  number={18},
  pages={2684--2685},
  year={2014},
  publisher={Oxford University Press}
}

@article{Huang2014,
title = "Search strategies and evaluation in protein-protein docking: principles, advances and challenges ",
journal = "Drug Discovery Today",
volume = "19",
number = "8",
pages = "1081--1096",
year = "2014",
issn = "1359-6446",
url = "http://www.sciencedirect.com/science/article/pii/S1359644614000579",
author = "Sheng-You Huang",
}

@Article{Malhotra2015,
author="Malhotra, Sony and Mathew, Oommen K. and Sowdhamini, Ramanathan",
title="{DOCKSCORE}: a webserver for ranking protein-protein docked poses",
journal="BMC Bioinformatics",
year="2015",
volume="16",
number="1",
pages="1--6",
issn="1471-2105",
}

@Article{Jeanquartier2015,
author="Jeanquartier, Fleur and Jean-Quartier, Claire and Holzinger, Andreas",
title="Integrated web visualizations for protein-protein interaction databases",
journal="BMC Bioinformatics",
year="2015",
volume="16",
number="1",
pages="1--16",
issn="1471-2105",
}

@article{Jin2014,
author = {Lingyan Jin and Weiru Wang and Guowei Fang},
title = {Targeting Protein-Protein Interaction by Small Molecules},
journal = {Annual Review of Pharmacology and Toxicology},
volume = {54},
number = {1},
pages = {435-456},
year = {2014},
}

@incollection{Varshney2003,
author = "Chang Ha Lee and Amitabh Varshney",
title = "Computing and Displaying Intermolecular Negative Volume for Docking",
booktitle = "Scientific Visualization:  The Visual Extraction of Knowledge from Data",
year = "2005",
pages={49--64},
publisher = "Springer",
address = "\hspace{-0.5em}",
}

@article{pdbsum,
    author = {Laskowski, Roman A. and Hutchinson, Gail E. and Michie, Alex D. and Wallace, Andrew C. and Jones, Martin L. and Thornton, Janet M.},
    journal = {Trends in Biochemical Sciences},
    number = {12},
    pages = {488--490},
    title = {P{D}{B}sum: a Web-based database of summaries and analyses of all {P}{D}{B} structures.},
    volume = {22},
    year = {1997},
}

@article{haddock,
author = {Cyril Dominguez and Rolf Boelens and Alexandre M. J. J. Bonvin},
title = {{HADDOCK}: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information},
journal = {Journal of the American Chemical Society},
volume = {125},
number = {7},
pages = {1731--1737},
year = {2003},
}

@article{Shindyalov1998,
author = {Shindyalov, I. N. and Bourne, P. E.}, 
title = {Protein structure alignment by incremental combinatorial extension {(CE)} of the optimal path.},
volume = {11}, 
number = {9}, 
pages = {739-747}, 
year = {1998}, 
URL = {http://peds.oxfordjournals.org/content/11/9/739.abstract}, 
journal = {Protein Engineering} ,
}

@Article{Palecek2015,
   Author="Palecek, J. J.  and Gruber, S. ",
   Title="{{K}ite {P}roteins: a {S}uperfamily of {S}{M}{C}/{K}leisin {P}artners {C}onserved {A}cross {B}acteria, {A}rchaea, and {E}ukaryotes}",
   Journal="Structure",
   Year="2015",
   Volume="23",
   Number="12",
   Pages="2183--2190",
}

@Article{Guerineau2012,
   Author="Guerineau, M.  and Kriz, Z.  and Kozakova, L.  and Bednarova, K.  and Janos, P.  and Palecek, J. ",
   Title="{{A}nalysis of the {N}se3/{M}{A}{G}{E}-binding domain of the {N}se4/{E}{I}{D} family proteins}",
   Journal="PLoS ONE",
   Year="2012",
   Volume="7",
   Number="4",
   Pages="e35813"
}

@Article{Hudson2011,
   Author="Hudson, J. J.  and Bednarova, K.  and Kozakova, L.  and Liao, C.  and Guerineau, M.  and Colnaghi, R.  and Vidot, S.  and Marek, J.  and Bathula, S. R.  and Lehmann, A. R.  and Palecek, J. ",
   Title="{{I}nteractions between the {N}se3 and {N}se4 components of the {S}{M}{C}5-6 complex identify evolutionarily conserved interactions between {M}{A}{G}{E} and {E}{I}{D} {F}amilies}",
   Journal="PLoS ONE",
   Year="2011",
   Volume="6",
   Number="2",
   Pages="e17270"
}

@inproceedings{Rao1994,
  title = {The Table Lens: Merging Graphical and Symbolic Representations in an Interactive Focus + Context Visualization for Tabular Information},
  booktitle = {Proceedings of the {{ACM SIGCHI Conference}} on {{Human Factors}} in {{Computing Systems}} ({{CHI}} '94)},
  publisher = {{ACM}},
  author = {Rao, Ramana and Card, Stuart K.},
  year = {1994},
  pages = {318--322},
  address = "\hspace{-0.5em}",
 }

@article{Byska2015,
	title = {{MoleCollar} and {Tunnel} {Heat} {Map} {Visualizations} for {Conveying} {Spatio}-{Temporo}-{Chemical} {Properties} {Across} and {Along} {Protein} {Voids}},
	volume = {34},
	issn = {0167-7055 (print), 1467-8659 (electronic)},
	number = {3},
	journal = {Comput. Graph. Forum},
	author = {By\v{s}ka, Jan and Jur\v{c}\'{i}k, Adam and Gr\"{o}ller, M. Eduard and Viola, Ivan and Kozl\'{i}kov\'{a}, Barbora},
	year = {2015},
	pages = {1--10}
} 

@inproceedings{Kozlikova2015,
	title = {Visualization of {Biomolecular} {Structures}: {State} of the {Art}},
	booktitle = {Eurographics {Conference} on {Visualization} - {STARs}},
	author = {Kozl\'{i}kov\'{a}, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian},
	year = {2015},
	pages = {61--81},
  organization={The Eurographics Association}
 }


@incollection{patane2015state,
  title={{State-of-the-Art and Perspectives of Geometric and Implicit Modeling for Molecular Surfaces}},
  author={Patan{\'e}, Giuseppe and Spagnuolo, Michela},
  booktitle={Computational Electrostatics for Biological Applications},
  pages={157--176},
  year={2015},
  publisher={Springer}
}

@article{krone2016visual,
  title={{Visual Analysis of Biomolecular Cavities: State of the Art}},
  author={Krone, Michael and Kozl{\'\i}kov{\'a}, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, J{\'u}lius and Hege, H-C and Viola, Ivan},
  journal={Computer Graphics Forum},
  volume={35},
  number={3},
  pages={527--551},
  year={2016},
  organization={Wiley Online Library}
}

@inproceedings {Tominski2014,
booktitle = {EuroVis - STARs},
editor = {R. Borgo and R. Maciejewski and I. Viola},
title = {{A Survey on Interactive Lenses in Visualization}},
author = {Tominski, Christian and Gladisch, Stefan and Kister, Ulrike and Dachselt, Raimund and Schumann, Heidrun},
year = {2014},
publisher = {The Eurographics Association},
}

@ARTICLE{Bruckner2006,
  author = {Stefan Bruckner and M. Eduard Gr{\"o}ller},
  title = {Exploded Views for Volume Data},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  year = {2006},
  volume = {12},
  pages = {1077--1084},
  number = {5},
  event = {IEEE Visualization 2006},
  issn = {1077-2626},
  keywords = {exploded views, illustrative visualization, volume rendering},
  url = {http://www.cg.tuwien.ac.at/research/publications/2006/bruckner-2006-EVV/}
}

@article{Lex2012,
	title = {{StratomeX:} Visual Analysis of {Large-Scale} Heterogeneous Genomics Data for Cancer Subtype Characterization},
	volume = {31},
	issn = {0167-7055},
	number = {3},
	journal = {Computer Graphics Forum {(EuroVis} '12)},
	author = {Lex, Alexander and Streit, Marc and Schulz, {Hans-J\"{o}rg} and Partl, Christian and Schmalstieg, Dieter and Park, Peter J. and Gehlenborg, Nils},
	year = {2012},
	pages = {1175--1184}
}

@Article{Doyle2010,
   Author="Doyle, J. M.  and Gao, J.  and Wang, J.  and Yang, M.  and Potts, P. R. ",
   Title="{{M}{A}{G}{E}-{R}{I}{N}{G} protein complexes comprise a family of {E}3 ubiquitin ligases}",
   Journal="Molecular Cell",
   Year="2010",
   Volume="39",
   Number="6",
   Pages="963--974",
}

@Article{Zabrady2016,
   Author="Zabrady, K.  and Adamus, M.  and Vondrova, L.  and Liao, C.  and Skoupilova, H.  and Novakova, M.  and Jurcisinova, L.  and Alt, A.  and Oliver, A. W.  and Lehmann, A. R.  and Palecek, J. J. ",
   Title="{{C}hromatin association of the {S}{M}{C}5/6 complex is dependent on binding of its {N}{S}{E}3 subunit to {D}{N}{A}}",
   Journal="Nucleic Acids Research",
   Year="2016",
   Volume="44",
   Number="3",
   Pages="1064--1079",
}

@article{pydock,
author = {Jimenez-Garcia, Brian and Pons, Carles and Fernandez-Recio, Juan}, 
title = {{pyDockWEB}: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring},
volume = {29}, 
number = {13}, 
pages = {1698-1699}, 
year = {2013}, 
journal = {Bioinformatics} 
}

@Article{Gligoris,
   Author="Gligoris, T.  and Lowe, J. ",
   Title="{{S}tructural {I}nsights into {R}ing {F}ormation of {C}ohesin and {R}elated {S}mc {C}omplexes}",
   Journal="Trends in Cell Biology",
   Year="2016",
   Volume="26",
   Number="9",
   Pages="680--693",
}

@Article{Kozakova,
   Author="Kozakova, L.  and Vondrova, L.  and Stejskal, K.  and Charalabous, P.  and Kolesar, P.  and Lehmann, A. R.  and Uldrijan, S.  and Sanderson, C. M.  and Zdrahal, Z.  and Palecek, J. J. ",
   Title="{{T}he melanoma-associated antigen 1 ({M}{A}{G}{E}{A}1) protein stimulates the {E}3 ubiquitin-ligase activity of {T}{R}{I}{M}31 within a {T}{R}{I}{M}31-{M}{A}{G}{E}{A}1-{N}{S}{E}4 complex}",
   Journal="Cell Cycle",
   Year="2015",
   Volume="14",
   Number="6",
   Pages="920--930"
}

@article{Crabben,
author = {Saskia N. van der Crabben AND Marije P. Hennus AND Grant A. McGregor AND Deborah I. Ritter AND Sandesh C.S. Nagamani AND Owen S. Wells AND Magdalena Harakalov\'{a} AND Ivan K. Chinn AND Aaron Alt AND Lucie Vondrov\'{a} AND Ron Hochstenbach AND Joris M. van Montfrans AND Suzanne W. Terheggen-Lagro AND Stef van Lieshout AND Markus J. van Roosmalen AND Ivo Renkens AND Karen Duran AND Isaac J. Nijman AND Wigard P. Kloosterman AND Eric Hennekam AND Jordan S. Orange AND Peter M. van Hasselt AND David A. Wheeler AND Jan J. Palecek AND Alan R. Lehmann AND Antony W. Oliver AND Laurence H. Pearl AND Sharon E. Plon AND Johanne M. Murray AND Gijs van Haaften},
journal = {The Journal of Clinical Investigation},
publisher = {The American Society for Clinical Investigation},
title = {Destabilized {SMC5/6} complex leads to chromosome breakage syndrome with severe lung disease},
year = {2016},
volume = {126},
url = {https://www.jci.org/articles/view/82890},
pages = {2881-2892},
number = {8},
}

@book{alberts02molecular,
    author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff, Martin and Roberts, Keith and Walter, Peter},
    edition = {4},
    howpublished = {Hardcover},
    isbn = {0815332181},
    posted-at = {2006-06-09 22:44:14},
    priority = {2},
    publisher = {Garland Science},
    title = {{Molecular Biology of the Cell}},
    year = {2002},
    address = "\hspace{-0.5em}",
}

@Article{Gavin,
   Author="Gavin, A. C.  and Aloy, P.  and Grandi, P.  and Krause, R.  and Boesche, M.  and Marzioch, M.  and Rau, C.  and Jensen, L. J.  and Bastuck, S.  and Dumpelfeld, B.  and Edelmann, A.  and Heurtier, M. A.  and Hoffman, V.  and Hoefert, C.  and Klein, K.  and Hudak, M.  and Michon, A. M.  and Schelder, M.  and Schirle, M.  and Remor, M.  and Rudi, T.  and Hooper, S.  and Bauer, A.  and Bouwmeester, T.  and Casari, G.  and Drewes, G.  and Neubauer, G.  and Rick, J. M.  and Kuster, B.  and Bork, P.  and Russell, R. B.  and Superti-Furga, G. ",
   Title="{{P}roteome survey reveals modularity of the yeast cell machinery}",
   Journal="Nature",
   Year="2006",
   Volume="440",
   Number="7084",
   Pages="631--636",
}

@INPROCEEDINGS{480793, 
  title={Defining, computing, and visualizing molecular interfaces},
  author={Varshney, Amitabh and Brooks Jr, Frederick P and Manocha, Dinesh and Wright, William V and Richardson, David C},
  booktitle={Proceedings of the 6th conference on Visualization'95},
  pages={36--43},
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  organization={IEEE Computer Society}
}

@article{Ban2006,
  title={Interface surfaces for protein-protein complexes},
  author={Ban, Yih-En Andrew and Edelsbrunner, Herbert and Rudolph, Johannes},
  journal={Journal of the ACM (JACM)},
  volume={53},
  number={3},
  pages={361--378},
  year={2006},
  publisher={ACM}
} 

@Article{Woo,
   Author="Woo, J. S.  and Lim, J. H.  and Shin, H. C.  and Suh, M. K.  and Ku, B.  and Lee, K. H.  and Joo, K.  and Robinson, H.  and Lee, J.  and Park, S. Y.  and Ha, N. C.  and Oh, B. H. ",
   Title="{{S}tructural studies of a bacterial condensin complex reveal {A}{T}{P}-dependent disruption of intersubunit interactions}",
   Journal="Cell",
   Year="2009",
   Volume="136",
   Number="1",
   Pages="85--96",
   Month="Jan"
}

@Article{pmid25414305,
   Author="Gligoris, T. G.  and Scheinost, J. C.  and Burmann, F.  and Petela, N.  and Chan, K. L.  and Uluocak, P.  and Beckouet, F.  and Gruber, S.  and Nasmyth, K.  and Lowe, J. ",
   Title="{{C}losing the cohesin ring: structure and function of its {S}mc3-kleisin interface}",
   Journal="Science",
   Year="2014",
   Volume="346",
   Number="6212",
   Pages="963--967",
   Month="Nov"
}