{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T22:39:10Z","timestamp":1783636750820,"version":"3.55.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007207","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T00:00:00Z","timestamp":1567641600000}}],"reference-count":73,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T00:00:00Z","timestamp":1566518400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007207","type":"journal-article","created":{"date-parts":[[2019,8,23]],"date-time":"2019-08-23T17:37:50Z","timestamp":1566581870000},"page":"e1007207","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":108,"title":["Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces"],"prefix":"10.1371","volume":"15","author":[{"given":"Shira","family":"Warszawski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aliza","family":"Borenstein Katz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5548-7309","authenticated-orcid":true,"given":"Rosalie","family":"Lipsh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0719-8027","authenticated-orcid":true,"given":"Lev","family":"Khmelnitsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1913-3703","authenticated-orcid":true,"given":"Gili","family":"Ben Nissan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1147-6293","authenticated-orcid":true,"given":"Gabriel","family":"Javitt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orly","family":"Dym","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamar","family":"Unger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orli","family":"Knop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shira","family":"Albeck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2837-5897","authenticated-orcid":true,"given":"Ron","family":"Diskin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"Fass","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal","family":"Sharon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3177-7560","authenticated-orcid":true,"given":"Sarel J.","family":"Fleishman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,8,23]]},"reference":[{"key":"pcbi.1007207.ref001","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.jmb.2007.09.005","article-title":"Affinity Maturation Increases the Stability and Plasticity of the Fv Domain of Anti-protein Antibodies","volume":"374","author":"JP Acierno","year":"2007","journal-title":"J Mol Biol"},{"key":"pcbi.1007207.ref002","doi-asserted-by":"crossref","first-page":"1962","DOI":"10.1002\/jps.21592","article-title":"Developability assessment in pharmaceutical industry: An integrated group approach for selecting developable candidates","author":"V Saxena","year":"2009","journal-title":"Journal of Pharmaceutical Sciences"},{"key":"pcbi.1007207.ref003","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/nprot.2006.94","article-title":"Isolating and engineering human antibodies using yeast surface display","volume":"1","author":"G Chao","year":"2006","journal-title":"Nat Protoc"},{"key":"pcbi.1007207.ref004","doi-asserted-by":"crossref","first-page":"10701","DOI":"10.1073\/pnas.170297297","article-title":"Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity","volume":"97","author":"ET Boder","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref005","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/j.jmb.2004.08.019","article-title":"Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody","volume":"343","author":"KS Midelfort","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi.1007207.ref006","doi-asserted-by":"crossref","first-page":"45259","DOI":"10.1038\/srep45259","article-title":"Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability","volume":"7","author":"MC Julian","year":"2017","journal-title":"Sci Rep"},{"key":"pcbi.1007207.ref007","doi-asserted-by":"crossref","first-page":"3675","DOI":"10.3390\/molecules16053675","article-title":"High affinity, developability and functional size: The holy grail of combinatorial antibody library generation","author":"D Ponsel","year":"2011","journal-title":"Molecules"},{"key":"pcbi.1007207.ref008","doi-asserted-by":"crossref","first-page":"E572","DOI":"10.1208\/aapsj080366","article-title":"Protein aggregation and bioprocessing","volume":"8","author":"MEM Cromwell","year":"2006","journal-title":"AAPS J"},{"key":"pcbi.1007207.ref009","doi-asserted-by":"crossref","first-page":"E501","DOI":"10.1208\/aapsj080359","article-title":"Effects of protein aggregates: an immunologic perspective","volume":"8","author":"AS Rosenberg","year":"2006","journal-title":"AAPS J"},{"key":"pcbi.1007207.ref010","doi-asserted-by":"crossref","first-page":"787","DOI":"10.4161\/mabs.25269","article-title":"Developability studies before initiation of process development: improving manufacturability of monoclonal antibodies","volume":"5","author":"X Yang","year":"2013","journal-title":"MAbs"},{"key":"pcbi.1007207.ref011","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nri2747","article-title":"Strategies and challenges for the next generation of therapeutic antibodies","volume":"10","author":"A Beck","year":"2010","journal-title":"Nat Rev Immunol"},{"key":"pcbi.1007207.ref012","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1038\/nbt1336","article-title":"Computational design of antibody-affinity improvement beyond in vivo maturation","volume":"25","author":"SM Lippow","year":"2007","journal-title":"Nat Biotechnol"},{"key":"pcbi.1007207.ref013","doi-asserted-by":"crossref","first-page":"11937","DOI":"10.1073\/pnas.0904191106","article-title":"Design of therapeutic proteins with enhanced stability","volume":"106","author":"N Chennamsetty","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref014","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1073\/pnas.1616408114","article-title":"Biophysical properties of the clinical-stage antibody landscape","volume":"114","author":"T Jain","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref015","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1080\/19420862.2015.1017695","article-title":"Boosting antibody developability through rational sequence optimization","volume":"7","author":"D Seeliger","year":"2015","journal-title":"MAbs"},{"key":"pcbi.1007207.ref016","doi-asserted-by":"crossref","first-page":"10879","DOI":"10.1073\/pnas.1202866109","article-title":"General strategy for the generation of human antibody variable domains with increased aggregation resistance","volume":"109","author":"K Dudgeon","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref017","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1016\/j.chembiol.2012.01.018","article-title":"Structure-based design of supercharged, highly thermoresistant antibodies","volume":"19","author":"AE Miklos","year":"2012","journal-title":"Chem Biol"},{"key":"pcbi.1007207.ref018","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1038\/nbt1000","article-title":"Aggregation-resistant domain antibodies selected on phage by heat denaturation","volume":"22","author":"L Jespers","year":"2004","journal-title":"Nat Biotechnol"},{"key":"pcbi.1007207.ref019","doi-asserted-by":"crossref","first-page":"3539","DOI":"10.1073\/pnas.0400060101","article-title":"Structural mechanism for affinity maturation of an anti-lysozyme antibody","volume":"101","author":"A Cauerhff","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref020","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.molcel.2016.06.012","article-title":"Automated Structure-and Sequence-Based Design of Proteins for High Bacterial Expression and Stability","volume":"63","author":"A Goldenzweig","year":"2016","journal-title":"Mol Cell"},{"key":"pcbi.1007207.ref021","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1146\/annurev-biochem-062917-012102","article-title":"Principles of Protein Stability and Their Application in Computational Design","volume":"87","author":"A Goldenzweig","year":"2018","journal-title":"Annu Rev Biochem"},{"key":"pcbi.1007207.ref022","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1073\/pnas.1616903114","article-title":"One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen","volume":"114","author":"I Campeotto","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref023","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1073\/pnas.1115172109","article-title":"Automated selection of stabilizing mutations in designed and natural proteins","author":"B Borgo","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1007207.ref024","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nbt.2214","article-title":"Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing","volume":"30","author":"TA Whitehead","year":"2012","journal-title":"Nat Biotechnol"},{"key":"pcbi.1007207.ref025","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/nmeth.3027","article-title":"Deep mutational scanning: a new style of protein science","volume":"11","author":"DM Fowler","year":"2014","journal-title":"Nat Methods"},{"key":"pcbi.1007207.ref026","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/nmeth.1492","article-title":"High-resolution mapping of protein sequence-function relationships","volume":"7","author":"DM Fowler","year":"2010","journal-title":"Nat Methods"},{"key":"pcbi.1007207.ref027","doi-asserted-by":"crossref","first-page":"E486","DOI":"10.1073\/pnas.1613231114","article-title":"Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding","volume":"114","author":"P Koenig","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref028","doi-asserted-by":"crossref","first-page":"523","DOI":"10.4161\/mabs.24979","article-title":"Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing","volume":"5","author":"CM Forsyth","year":"2013","journal-title":"MAbs"},{"key":"pcbi.1007207.ref029","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.bbrc.2012.10.066","article-title":"Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning","volume":"428","author":"Y Fujino","year":"2012","journal-title":"Biochem Biophys Res Commun"},{"key":"pcbi.1007207.ref030","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.23156","article-title":"Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves","volume":"5","author":"RM Adams","year":"2016","journal-title":"Elife"},{"key":"pcbi.1007207.ref031","doi-asserted-by":"crossref","first-page":"8705","DOI":"10.1073\/pnas.1524648113","article-title":"Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21","volume":"113","author":"I Leung","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref032","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/B978-0-12-394292-0.00001-1","article-title":"Computational design of novel protein binders and experimental affinity maturation","volume":"523","author":"TA Whitehead","year":"2013","journal-title":"Methods Enzymol"},{"key":"pcbi.1007207.ref033","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1016\/0022-2836(94)90046-9","article-title":"Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1","volume":"243","author":"BC Braden","year":"1994","journal-title":"J Mol Biol"},{"key":"pcbi.1007207.ref034","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/S0065-2776(08)60364-8","article-title":"Structure of antibody-antigen complexes: implications for immune recognition","volume":"43","author":"PM Colman","year":"1988","journal-title":"Adv Immunol"},{"key":"pcbi.1007207.ref035","doi-asserted-by":"crossref","first-page":"13722","DOI":"10.1073\/pnas.0603282103","article-title":"Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics","volume":"103","author":"J Zimmermann","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1007207.ref036","doi-asserted-by":"crossref","first-page":"333","DOI":"10.4049\/jimmunol.177.1.333","article-title":"Trends in antibody sequence changes during the somatic hypermutation process","volume":"177","author":"LA Clark","year":"2006","journal-title":"J Immunol"},{"key":"pcbi.1007207.ref037","first-page":"B1","article-title":"Humanised antibodies","volume":"0460167","author":"JR Adair","year":"1995","journal-title":"European Patent"},{"key":"pcbi.1007207.ref038","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1002\/prot.24779","article-title":"AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences","volume":"83","author":"GD Lapidoth","year":"2015","journal-title":"Proteins"},{"key":"pcbi.1007207.ref039","doi-asserted-by":"crossref","first-page":"10900","DOI":"10.1073\/pnas.1707171114","article-title":"Principles for computational design of binding antibodies","volume":"114","author":"D Baran","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007207.ref040","doi-asserted-by":"crossref","first-page":"2780","DOI":"10.1038\/s41467-018-05205-5","article-title":"Highly active enzymes by automated combinatorial backbone assembly and sequence design","volume":"9","author":"G Lapidoth","year":"2018","journal-title":"Nat Commun"},{"key":"pcbi.1007207.ref041","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.molcel.2018.08.033","article-title":"Automated Design of Efficient and Functionally Diverse Enzyme Repertoires","volume":"72","author":"O Khersonsky","year":"2018","journal-title":"Mol Cell"},{"key":"pcbi.1007207.ref042","doi-asserted-by":"crossref","first-page":"5286","DOI":"10.1038\/s41467-018-07722-9","article-title":"Ultrahigh specificity in a network of computationally designed protein-interaction pairs","volume":"9","author":"R Netzer","year":"2018","journal-title":"Nat Commun"},{"key":"pcbi.1007207.ref043","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1002\/pro.2892","article-title":"Why reinvent the wheel? Building new proteins based on ready-made parts","volume":"25","author":"O Khersonsky","year":"2016","journal-title":"Protein Sci"},{"key":"pcbi.1007207.ref044","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/protein\/gzq043","article-title":"Analysis and prediction of VH\/VL packing in antibodies","volume":"23","author":"KR Abhinandan","year":"2010","journal-title":"Protein Eng Des Sel"},{"key":"pcbi.1007207.ref045","doi-asserted-by":"crossref","first-page":"6625","DOI":"10.1074\/jbc.M507783200","article-title":"Structure-Function Studies of Two Synthetic Anti-vascular Endothelial Growth Factor Fabs and Comparison with the Avastin Fab","volume":"281","author":"G Fuh","year":"2006","journal-title":"J Biol Chem"},{"key":"pcbi.1007207.ref046","doi-asserted-by":"crossref","first-page":"3307","DOI":"10.1038\/onc.2009.181","article-title":"Loss of Nkx3.1 leads to the activation of discrete downstream target genes during prostate tumorigenesis","volume":"28","author":"H Song","year":"2009","journal-title":"Oncogene"},{"key":"pcbi.1007207.ref047","doi-asserted-by":"crossref","first-page":"4366","DOI":"10.1016\/j.jmb.2013.07.011","article-title":"An inhibitory antibody blocks the first step in the dithiol\/disulfide relay mechanism of the enzyme QSOX1","volume":"425","author":"I Grossman","year":"2013","journal-title":"J Mol Biol"},{"key":"pcbi.1007207.ref048","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nature11267","article-title":"The dynamic disulphide relay of quiescin sulphydryl oxidase","volume":"488","author":"A Alon","year":"2012","journal-title":"Nature"},{"key":"pcbi.1007207.ref049","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/j.jmb.2004.05.051","article-title":"High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold","volume":"340","author":"CV Lee","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi.1007207.ref050","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1002\/prot.22921","article-title":"Role of conformational sampling in computing mutation-induced changes in protein structure and stability","volume":"79","author":"EH Kellogg","year":"2011","journal-title":"Proteins"},{"key":"pcbi.1007207.ref051","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1038\/nmeth0607-466","article-title":"Eris: an automated estimator of protein stability","volume":"4","author":"S Yin","year":"2007","journal-title":"Nat Methods"},{"key":"pcbi.1007207.ref052","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1002\/jps.24430","article-title":"Developability assessment during the selection of novel therapeutic antibodies","volume":"104","author":"A Jarasch","year":"2015","journal-title":"J Pharm Sci"},{"key":"pcbi.1007207.ref053","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1126\/science.aad8865","article-title":"De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity","volume":"352","author":"SE Boyken","year":"2016","journal-title":"Science"},{"key":"pcbi.1007207.ref054","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1126\/science.aaf7599","article-title":"Inspired by nature: designed proteins have structural features resembling those of natural active sites","volume":"352","author":"R Netzer","year":"2016","journal-title":"Science"},{"key":"pcbi.1007207.ref055","author":"G Ben-Nissan","journal-title":"Rapid Characterization of Secreted Recombinant Proteins"},{"key":"pcbi.1007207.ref056","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.freeradbiomed.2014.01.020","article-title":"Disulfide bond generation in mammalian blood serum: detection and purification of quiescin-sulfhydryl oxidase","volume":"69","author":"BA Israel","year":"2014","journal-title":"Free Radic Biol Med"},{"key":"pcbi.1007207.ref057","doi-asserted-by":"crossref","first-page":"2858","DOI":"10.1111\/j.1742-4658.2011.08207.x","article-title":"The association of heavy and light chain variable domains in antibodies: implications for antigen specificity","volume":"278","author":"A Chailyan","year":"2011","journal-title":"FEBS J"},{"key":"pcbi.1007207.ref058","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1002\/prot.24567","article-title":"Second antibody modeling assessment (AMA-II)","volume":"82","author":"JC Almagro","year":"2014","journal-title":"Proteins: Struct Funct Bioinf"},{"key":"pcbi.1007207.ref059","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1002\/prot.25185","article-title":"High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments","volume":"85","author":"CH Norn","year":"2017","journal-title":"Proteins"},{"issue":"9","key":"pcbi.1007207.ref060","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1093\/bioinformatics\/bty822","article-title":"AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains","volume":"35","author":"G Lapidoth","year":"2019","journal-title":"Bioinformatics"},{"key":"pcbi.1007207.ref061","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1126\/science.1546293","article-title":"Structural evidence for induced fit as a mechanism for antibody-antigen recognition","volume":"255","author":"JM Rini","year":"1992","journal-title":"Science"},{"key":"pcbi.1007207.ref062","doi-asserted-by":"crossref","first-page":"2643","DOI":"10.1021\/ja01867a018","article-title":"A theory of the structure and process of formation of antibodies","volume":"62","author":"L Pauling","year":"1940","journal-title":"J Am Chem Soc"},{"key":"pcbi.1007207.ref063","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/0969-2126(93)90024-B","article-title":"Major antigen-induced domain rearrangements in an antibody","volume":"1","author":"RL Stanfield","year":"1993","journal-title":"Structure"},{"key":"pcbi.1007207.ref064","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.12125","article-title":"Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane","volume":"5","author":"A Elazar","year":"2016","journal-title":"Elife"},{"key":"pcbi.1007207.ref065","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1186\/1472-6750-8-91","article-title":"An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol","volume":"8","author":"H Liu","year":"2008","journal-title":"BMC Biotechnol"},{"key":"pcbi.1007207.ref066","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nprot.2007.17","article-title":"Frozen competent yeast cells that can be transformed with high efficiency using the LiAc\/SS carrier DNA\/PEG method","volume":"2","author":"RD Gietz","year":"2007","journal-title":"Nat Protoc"},{"key":"pcbi.1007207.ref067","doi-asserted-by":"crossref","first-page":"e20161","DOI":"10.1371\/journal.pone.0020161","article-title":"RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite","volume":"6","author":"SJ Fleishman","year":"2011","journal-title":"PLoS One"},{"key":"pcbi.1007207.ref068","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1021\/ct500864r","article-title":"Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta","volume":"11","author":"MJ O\u2019Meara","year":"2015","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1007207.ref069","doi-asserted-by":"crossref","first-page":"6201","DOI":"10.1021\/acs.jctc.6b00819","article-title":"Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules","volume":"12","author":"H Park","year":"2016","journal-title":"J Chem Theory Comput"},{"key":"pcbi.1007207.ref070","doi-asserted-by":"crossref","first-page":"4708","DOI":"10.1021\/acs.analchem.7b00518","article-title":"Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex","volume":"89","author":"G Ben-Nissan","year":"2017","journal-title":"Anal Chem"},{"key":"pcbi.1007207.ref071","article-title":"Analyzing large protein complexes by structural mass spectrometry","author":"N Kirshenbaum","year":"2010","journal-title":"J Vis Exp"},{"key":"pcbi.1007207.ref072","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.jim.2007.09.017","article-title":"Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning","volume":"329","author":"T Tiller","year":"2008","journal-title":"J Immunol Methods"},{"key":"pcbi.1007207.ref073","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.jsb.2010.06.016","article-title":"Applications of the Restriction Free (RF) cloning procedure for molecular manipulations and protein expression","volume":"172","author":"T Unger","year":"2010","journal-title":"J Struct Biol"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007207","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T00:00:00Z","timestamp":1567641600000}},{"DOI":"10.1371\/journal.pcbi.1008382","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T00:00:00Z","timestamp":1603238400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007207","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T12:14:41Z","timestamp":1589026481000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007207"}},"subtitle":[],"editor":[{"given":"Ozlem","family":"Keskin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,8,23]]},"references-count":73,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2019,8,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007207","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1007207","asserted-by":"object"}],"correction":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1008382","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,23]]}}}