{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T11:45:25Z","timestamp":1792151125677,"version":"4.4.0"},"reference-count":54,"publisher":"American Chemical Society (ACS)","issue":"3","license":[{"start":{"date-parts":[[2020,3,13]],"date-time":"2020-03-13T00:00:00Z","timestamp":1584057600000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_ccby_termsofuse.html"}],"funder":[{"DOI":"10.13039\/501100004063","name":"Knut och Alice Wallenbergs Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007863","name":"Rice University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007863","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We define a molecular caging complex as a pair of molecules in which one molecule (the \u201chost\u201d or \u201ccage\u201d) possesses a cavity that can encapsulate the other molecule (the \u201cguest\u201d) and prevent it from escaping. Molecular caging complexes can be useful in applications such as molecular shape sorting, drug delivery, and molecular immobilization in materials science, to name just a few. However, the design and computational discovery of new caging complexes is a challenging task, as it is hard to predict whether one molecule can encapsulate another because their shapes can be quite complex. In this paper, we propose a computational screening method that predicts whether a given pair of molecules form a caging complex. Our method is based on a caging verification algorithm that was designed by our group for applications in robotic manipulation. We tested our algorithm on three pairs of molecules that were previously described in a pioneering work on molecular caging complexes and found that our results are fully consistent with the previously reported ones. Furthermore, we performed a screening experiment on a data set consisting of 46 hosts and four guests and used our algorithm to predict which pairs are likely to form caging complexes. Our method is computationally efficient and can be integrated into a screening pipeline to complement experimental techniques.<\/jats:p>","DOI":"10.1021\/acs.jcim.9b00945","type":"journal-article","created":{"date-parts":[[2020,3,4]],"date-time":"2020-03-04T17:48:32Z","timestamp":1583344112000},"page":"1302-1316","source":"Crossref","is-referenced-by-count":8,"title":["A Robotics-Inspired Screening Algorithm for Molecular\nCaging Prediction"],"prefix":"10.1021","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9001-7708","authenticated-orcid":true,"given":"Oleksandr","family":"Kravchenko","sequence":"first","affiliation":[{"name":"KTH Royal Institute of Technology , , ,","place":["Stockholm, Sweden, 11428"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasiia","family":"Varava","sequence":"additional","affiliation":[{"name":"KTH Royal Institute of Technology , , ,","place":["Stockholm, Sweden, 10044"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1114-6040","authenticated-orcid":true,"given":"Florian T.","family":"Pokorny","sequence":"additional","affiliation":[{"name":"KTH Royal Institute of Technology , , ,","place":["Stockholm, Sweden, 10044"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3415-9816","authenticated-orcid":true,"given":"Didier","family":"Devaurs","sequence":"additional","affiliation":[{"name":"Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP (Institute of Engineering, Universite\u0301 Grenoble Alpes), LJK , ,","place":["Grenoble, France, 38000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0699-8038","authenticated-orcid":true,"given":"Lydia E.","family":"Kavraki","sequence":"additional","affiliation":[{"name":"Rice University , , , ,","place":["Houston, Texas, United States, 77005"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2965-2953","authenticated-orcid":true,"given":"Danica","family":"Kragic","sequence":"additional","affiliation":[{"name":"KTH Royal Institute of Technology , , ,","place":["Stockholm, Sweden, 10044"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,3,4]]},"reference":[{"key":"2026101606213668100_cit1","doi-asserted-by":"publisher","first-page":"1308","DOI":"10.1126\/science.1096914","article-title":"Molecular Borromean Rings","volume":"304","author":"Chichak","year":"2004","journal-title":"Science"},{"key":"2026101606213668100_cit2","doi-asserted-by":"publisher","first-page":"16053","DOI":"10.1038\/natrevmats.2016.53","article-title":"Porous Organic Cages: Soluble, Modular and Molecular\nPores","volume":"1","author":"Hasell","year":"2016","journal-title":"Nat. Rev. Mater."},{"key":"2026101606213668100_cit3","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1126\/science.219.4589.1177","article-title":"Cavitands:\nOrganic Hosts with Enforced Cavities","volume":"219","author":"Cram","year":"1983","journal-title":"Science"},{"key":"2026101606213668100_cit4","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.ccr.2016.07.007","article-title":"Supramolecular Nanoreactors\nfor Catalysis","volume":"324","author":"Deraedt","year":"2016","journal-title":"Coord. Chem. Rev."},{"key":"2026101606213668100_cit5","doi-asserted-by":"publisher","first-page":"5042","DOI":"10.1002\/anie.201000443","article-title":"Shape-Persistent\nOrganic Cage Compounds by Dynamic Covalent Bond Formation","volume":"49","author":"Mastalerz","year":"2010","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026101606213668100_cit6","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1002\/anie.201207373","article-title":"Light-Triggered Guest Uptake and\nRelease by a Photochromic Coordination Cage","volume":"52","author":"Han","year":"2013","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026101606213668100_cit7","doi-asserted-by":"publisher","first-page":"1746","DOI":"10.1002\/anie.201509265","article-title":"Reversible\nGuest Uptake\/Release by Redox-Controlled Assembly\/Disassembly of a\nCoordination Cage","volume":"55","author":"Croue\u0301","year":"2016","journal-title":"Angew. Chem., Int. Ed."},{"key":"2026101606213668100_cit8","doi-asserted-by":"publisher","DOI":"10.1038\/am.2016.128","article-title":"Engineering Protein\nNanocages as Carriers for Biomedical Applications","volume":"9","author":"Bhaskar","year":"2017","journal-title":"NPG Asia Mater."},{"key":"2026101606213668100_cit9","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1039\/C4CS00222A","article-title":"Metal-Organic Molecular\nCages: Applications of Biochemical Implications","volume":"44","author":"Ahmad","year":"2015","journal-title":"Chem. Soc. Rev."},{"key":"2026101606213668100_cit10","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1007\/128_2011_272","article-title":"Drug Delivery\nby Water-Soluble Organometallic Cages","volume":"319","author":"Therrien","year":"2011","journal-title":"Top.\nCurr. Chem."},{"key":"2026101606213668100_cit11","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.2217\/nnm.14.67","article-title":"Synthetic and Bioinspired Cage Nanoparticles for Drug Delivery","volume":"9","author":"Deshayes","year":"2014","journal-title":"Nanomedicine"},{"key":"2026101606213668100_cit12","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/nchem.1550","article-title":"Molecular Shape Sorting Using Molecular\nOrganic Cages","volume":"5","author":"Mitra","year":"2013","journal-title":"Nat. Chem."},{"key":"2026101606213668100_cit13","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1038\/nmat4035","article-title":"Separation of Rare Gases,\nChiral Molecules by Selective Binding in\nPorous Organic Cages","volume":"13","author":"Chen","year":"2014","journal-title":"Nat. Mater."},{"key":"2026101606213668100_cit14","doi-asserted-by":"publisher","first-page":"2411","DOI":"10.1021\/acs.accounts.8b00298","article-title":"Porous Shape-Persistent\nOrganic Cage Compounds of Different Size, Geometry, and Function","volume":"51","author":"Mastalerz","year":"2018","journal-title":"Acc. Chem. Res."},{"key":"2026101606213668100_cit15","doi-asserted-by":"publisher","first-page":"973","DOI":"10.1038\/nmat2545","article-title":"Porous Organic Cages","volume":"8","author":"Tozawa","year":"2009","journal-title":"Nat. Mater."},{"key":"2026101606213668100_cit16","doi-asserted-by":"publisher","first-page":"2849","DOI":"10.1038\/s41467-018-05271-9","article-title":"High-throughput\nDiscovery of Organic Cages and Catenanes Using Computational Screening\nFused with Robotic Synthesis","volume":"9","author":"Greenaway","year":"2018","journal-title":"Nat. Commun."},{"key":"2026101606213668100_cit17","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1021\/acs.chemmater.8b03572","article-title":"Machine Learning for Organic Cage\nProperty Prediction","volume":"31","author":"Turcani","year":"2019","journal-title":"Chem. Mater."},{"key":"2026101606213668100_cit18","unstructured":"Varava, A.; Carvalho, J. F.; Pokorny, F. T.; Kragic, D.\n          Caging and Path\nNon-Existence: A Deterministic Sampling-Based Verification Algorithm. Presented at the International Symposium on Robotics Research, 2017."},{"key":"2026101606213668100_cit19","unstructured":"Varava, A.; Carvalho, J. F.; Pokorny, F. T.; Kragic, D.\n          Free\nSpace of\nRigid Objects: Caging, Path Non-Existence, and Narrow Passage Detection. Presented at the Workshop on the Algorithmic Foundations of Robotics, 2018."},{"key":"2026101606213668100_cit20","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1080\/01691864.2017.1371075","article-title":"A Survey of Robotic\nCaging and Its Applications","volume":"31","author":"Makita","year":"2017","journal-title":"Adv. Rob."},{"key":"2026101606213668100_cit21","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1016\/j.micromeso.2011.08.020","article-title":"Algorithms\nand Tools for High-Throughput Geometry-Based Analysis of Crystalline\nPorous Materials","volume":"149","author":"Willems","year":"2012","journal-title":"Microporous Mesoporous Mater."},{"key":"2026101606213668100_cit22","doi-asserted-by":"publisher","first-page":"8328","DOI":"10.1038\/ncomms9328","article-title":"In Silico Prediction\nand Screening of Modular Crystal Structures via a High-Throughput\nGenomic Approach","volume":"6","author":"Li","year":"2015","journal-title":"Nat. Commun."},{"key":"2026101606213668100_cit23","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1613\/jair.5040","article-title":"A Survey of Computational\nTreatments of Biomolecules by Robotics-Inspired\nMethods Modeling Equilibrium Structure and Dynamic","volume":"57","author":"Shehu","year":"2016","journal-title":"Journal of Artificial Intelligence Research"},{"key":"2026101606213668100_cit24","doi-asserted-by":"publisher","first-page":"W297","DOI":"10.1093\/nar\/gkt380","article-title":"MoMA-LigPath:\na Web Server to Simulate Protein\u2013Ligand Unbinding","volume":"41","author":"Devaurs","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2026101606213668100_cit25","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1038\/nature16072","article-title":"Liquids with Permanent Porosity","volume":"527","author":"Giri","year":"2015","journal-title":"Nature"},{"key":"2026101606213668100_cit26","doi-asserted-by":"publisher","first-page":"10841","DOI":"10.1002\/ange.201105104","article-title":"Large Self-Assembled\nChiral Organic Cages: Synthesis,\nStructure, and Shape Persistence","volume":"123","author":"Jelfs","year":"2011","journal-title":"Angew. Chem."},{"key":"2026101606213668100_cit27","doi-asserted-by":"publisher","first-page":"15211","DOI":"10.1021\/acs.jpcc.7b03848","article-title":"Computational Screening\nof Porous Organic Molecules\nfor Xenon\/Krypton Separation","volume":"121","author":"Miklitz","year":"2017","journal-title":"J. Phys. Chem.\nC"},{"key":"2026101606213668100_cit28","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1126\/science.283.5405.1145","article-title":"Supertetrahedral\nSulfide Crystals with Giant Cavities and Channels","volume":"283","author":"Li","year":"1999","journal-title":"Science"},{"key":"2026101606213668100_cit29","doi-asserted-by":"publisher","first-page":"7528","DOI":"10.1021\/ja1023699","article-title":"Efficient Calculation\nof Diffusion\nLimitations in Metal Organic Framework Materials: A Tool for Identifying\nMaterials for Kinetic Separations","volume":"132","author":"Haldoupis","year":"2010","journal-title":"J. Am. Chem.\nSoc."},{"key":"2026101606213668100_cit30","doi-asserted-by":"publisher","first-page":"2217","DOI":"10.1039\/c2sc01097f","article-title":"Thermodynamic Analysis\nof Xe\/Kr Selectivity in over 137000 Hypothetical Metal-Organic Frameworks","volume":"3","author":"Sikora","year":"2012","journal-title":"Chem. Sci."},{"key":"2026101606213668100_cit31","doi-asserted-by":"publisher","first-page":"5735","DOI":"10.1039\/C4CS00070F","article-title":"High-Throughput Computational Screening of Metal-Organic\nFrameworks","volume":"43","author":"Colo\u0301n","year":"2014","journal-title":"Chem. Soc. Rev."},{"key":"2026101606213668100_cit32","doi-asserted-by":"publisher","first-page":"7531","DOI":"10.1039\/c3ce41057a","article-title":"High Accuracy\nGeometric Analysis of Crystalline Porous Materials","volume":"15","author":"Pinheiro","year":"2013","journal-title":"CrystEngComm"},{"key":"2026101606213668100_cit33","doi-asserted-by":"publisher","first-page":"2387","DOI":"10.1021\/acs.jcim.8b00490","article-title":"pywindow: Automated Structural Analysis of Molecular\nPores","volume":"58","author":"Miklitz","year":"2018","journal-title":"J. Chem. Inf. Model."},{"key":"2026101606213668100_cit34","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1039\/b803498m","article-title":"Using Molecular\nSimulation to Characterise\nMetal-Organic Frameworks for Adsorption Applications","volume":"38","author":"Du\u0308ren","year":"2009","journal-title":"Chem. Soc. Rev."},{"key":"2026101606213668100_cit35","doi-asserted-by":"publisher","first-page":"16639","DOI":"10.1021\/jp305129w","article-title":"Bespoke\nForce Field for Simulating the Molecular Dynamics of Porous Organic\nCages","volume":"116","author":"Holden","year":"2012","journal-title":"J. Phys. Chem. C"},{"key":"2026101606213668100_cit36","doi-asserted-by":"publisher","first-page":"14114","DOI":"10.1021\/la301915s","article-title":"Accelerating Applications\nof Metal-Organic Frameworks\nfor Gas Adsorption and Separation by Computational Screening of Materials","volume":"28","author":"Watanabe","year":"2012","journal-title":"Langmuir"},{"key":"2026101606213668100_cit37","doi-asserted-by":"publisher","first-page":"1663","DOI":"10.1021\/acscentsci.8b00638","article-title":"Eigencages: Learning\na Latent Space of Porous Cage Molecules","volume":"4","author":"Sturluson","year":"2018","journal-title":"ACS\nCent. Sci."},{"key":"2026101606213668100_cit38","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1016\/j.micromeso.2010.10.019","article-title":"Reverse\nShape Selectivity in the Adsorption of Hexane and Xylene Isomers in\nMOF UiO-66","volume":"139","author":"Ba\u0301rcia","year":"2011","journal-title":"Microporous Mesoporous Mater."},{"key":"2026101606213668100_cit39","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1177\/0278364912442972","article-title":"From Caging\nto Grasping","volume":"31","author":"Rodriguez","year":"2012","journal-title":"Int. J. Rob. Res."},{"key":"2026101606213668100_cit40","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/3-540-36268-1_25","article-title":"Cooperative\nTransport of Planar Objects by Multiple Mobile Robots Using Object\nClosure","volume-title":"Experimental Robotics VIII","author":"Pereira","year":"2003"},{"key":"2026101606213668100_cit41","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1177\/0278364904045477","article-title":"Decentralized\nAlgorithms for Multi-Robot\nManipulation via Caging","volume":"23","author":"Pereira","year":"2004","journal-title":"Int. J. Rob. Res."},{"key":"2026101606213668100_cit42","first-page":"7","volume-title":"Molecular Modelling:\nPrinciples and Applications","author":"Leach","year":"2001"},{"key":"2026101606213668100_cit43","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1021\/j100785a001","article-title":"van der Waals\nVolumes and Radii","volume":"68","author":"Bondi","year":"1964","journal-title":"J. Phys. Chem."},{"key":"2026101606213668100_cit44","doi-asserted-by":"publisher","first-page":"7384","DOI":"10.1021\/jp953141+","article-title":"Intermolecular Nonbonded\nContact Distances in Organic\nCrystal Structures: Comparison with Distances Expected from van der\nWaals Radii","volume":"100","author":"Rowland","year":"1996","journal-title":"J. Phys. Chem."},{"key":"2026101606213668100_cit45","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1177\/0278364909352700","article-title":"Generating Uniform\nIncremental Grids on SO(3) Using the Hopf Fibration","volume":"29","author":"Yershova","year":"2010","journal-title":"Int. J. Rob. Res."},{"key":"2026101606213668100_cit46","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1007\/PL00009412","article-title":"Deformable\nSmooth Surface Design","volume":"21","author":"Edelsbrunner","year":"1999","journal-title":"Discrete Comp. Geom."},{"key":"2026101606213668100_cit47","doi-asserted-by":"publisher","first-page":"2524","DOI":"10.1039\/c3cc39098e","article-title":"Self-Assembly\nof a Covalent Organic Cage with Exceptionally Large and Symmetrical\nInterior Cavity: the Role of Entropy of Symmetry","volume":"49","author":"Skowronek","year":"2013","journal-title":"Chem. Commun."},{"key":"2026101606213668100_cit48","doi-asserted-by":"publisher","first-page":"5598","DOI":"10.1021\/cg201173j","article-title":"Cucurbit[n]urils\n(n = 58): A Comprehensive Solid State Study","volume":"11","author":"Bardelang","year":"2011","journal-title":"Cryst. Growth Des."},{"key":"2026101606213668100_cit49","doi-asserted-by":"publisher","first-page":"16452","DOI":"10.1021\/ja509880v","article-title":"All-Benzene Carbon Nanocages: Size-Selective\nSynthesis, Photophysical Properties, and Crystal Structure","volume":"136","author":"Matsui","year":"2014","journal-title":"J. Am. Chem. Soc."},{"key":"2026101606213668100_cit50","first-page":"450","volume-title":"Encyclopedia of Supramolecular Chemistry","author":"Atwood","year":"2004"},{"key":"2026101606213668100_cit51","doi-asserted-by":"publisher","first-page":"5280","DOI":"10.1039\/C7NR00703E","article-title":"Topological Landscapes\nof Porous Organic Cages","volume":"9","author":"Santolini","year":"2017","journal-title":"Nanoscale"},{"key":"2026101606213668100_cit52","first-page":"1","article-title":"Geometric Models of Protein\nStructure and Function Prediction","volume-title":"Models\nand Algorithms for Biomolecules and Molecular Networks","author":"Dasgupta","year":"2016"},{"key":"2026101606213668100_cit53","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1109\/LRA.2016.2519145","article-title":"Energy-Bounded Caging: Formal Definition\nand 2-D Energy\nLower Bound Algorithm Based on Weighted Alpha Shapes","volume":"1","author":"Mahler","year":"2016","journal-title":"IEEE Robot. Autom. Lett."},{"key":"2026101606213668100_cit54","doi-asserted-by":"publisher","first-page":"1479","DOI":"10.1109\/TRO.2016.2602374","article-title":"Caging\nGrasps of Rigid and Partially\nDeformable 3-D Objects With Double Fork and Neck Features","volume":"32","author":"Varava","year":"2016","journal-title":"IEEE Trans. Robot."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.9b00945","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/3\/1302\/68674103\/acs.jcim.9b00945.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/3\/1302\/68674103\/acs.jcim.9b00945.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T10:49:12Z","timestamp":1792147752000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/60\/3\/1302\/862878\/A-Robotics-Inspired-Screening-Algorithm-for"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,4]]},"references-count":54,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3,4]]},"published-print":{"date-parts":[[2020,3,23]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.9b00945","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,4]]}}}