VU Gyvybės mokslų centro autoriaus 'Justas Dapkūnas' publikacijų sąrašas

2024
1 Dapkūnas, Justas; Timinskas, Albertas; Olechnovič, Kliment; Tomkuvienė, Miglė; Venclovas, Česlovas. PPI3D: a web server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions // Nucleic acids research. Oxford : Oxford University Press. ISSN 0305-1048. eISSN 1362-4962. 2024, vol. 52, iss. W1, art. no. gkae278, p. W264-W271. DOI: 10.1093/nar/gkae278. [DB: Science Citation Index Expanded (Web of Science)]
2 Žebrauskienė, Dovilė; Sadauskienė, Eglė; Dapkūnas, Justas; Kairys, Visvaldas; Balčiūnas, Joris; Konovalovas, Aleksandras; Masiulienė, Rūta; Petraitytė, Gunda; Valevičienė, Nomeda Rima; Matačiūnas, Mindaugas; Barysienė, Jūratė; Mikštienė, Violeta; Tomkuvienė, Miglė; Preikšaitienė, Eglė. Aortic disease and cardiomyopathy in patients with a novel DNMT3A gene variant causing Tatton-Brown–Rahman syndrome // Clinical epigenetics. London : BioMed Central Ltd. ISSN 1868-7075. eISSN 1868-7083. 2024, vol. 16, iss. 1, art. no. 76, p. [1-15]. DOI: 10.1186/s13148-024-01686-y. [DB: Science Citation Index Expanded (Web of Science), Scopus]

2023
1 Dapkūnas, Justas; Margelevičius, Mindaugas. The COMER web server for protein analysis by homology // Bioinformatics. Oxford : Oxford University Press. ISSN 1367-4803. eISSN 1460-2059. 2023, vol. 39, no. 1, art. no. btac807, p. [1-3]. DOI: 10.1093/bioinformatics/btac807. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 4.400; AIF: 4.066; Q1 (2023 InCities JCR SCIE)]
2 Olechnovič, Kliment; Valančauskas, Lukas; Dapkūnas, Justas; Venclovas, Česlovas. Prediction of protein assemblies by structure sampling followed by interface-focused scoring // Proteins - structure function and bioinformatics: Special issue:CASP15: Critical Assessment of methods for Structure Prediction, 15th round. Hoboken : Wiley. eISSN 1097-0134. 2023, vol. 91, iss. 12, p. 1724-1733. DOI: 10.1002/prot.26569. [DB: Science Citation Index Expanded (Web of Science)]
3 Lensink, Marc F.; Brysbaert, Guillaume; Raouraoua, Nessim; Bates, Paul A.; Giulini, Marco; Honorato, Rodrigo V.; van Noort, Charlotte; Teixeira, Joao M. C.; Bonvin, Alexandre M. J. J.; Kong, Ren; Shi, Hang; Lu, Xufeng; Chang, Shan; Liu, Jian; Guo, Zhiye; Chen, Xiao; Morehead, Alex; Roy, Raj S.; Wu, Tianqi; Giri, Nabin; Quadir, Farhan; Chen, Chen; Cheng, Jianlin; Del Carpio, Carlos A.; Ichiishi, Eichiro; Rodriguez-Lumbreras, Luis A.; Fernandez-Recio, Juan; Harmalkar, Ameya; Chu, Lee-Shin; Canner, Sam; Smanta, Rituparna; Gray, Jeffrey J.; Li, Hao; Lin, Peicong; He, Jiahua; Tao, Huanyu; Huang, Sheng-You; Roel-Touris, Jorge; Jimenez-Garcia, Brian; Christoffer, Charles W.; Jain, Anika J.; Kagaya, Yuki; Kannan, Harini; Nakamura, Tsukasa; Terashi, Genki; Verburgt, Jacob C.; Zhang, Yuanyuan; Zhang, Zicong; Fujuta, Hayato; Sekijima, Masakazu; Kihara, Daisuke; Khan, Omeir; Kotelnikov, Sergei; Ghani, Usman; Padhorny, Dzmitry; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima; Negi, Surendra S.; Ricciardelli, Tiziana; Barradas-Bautista, Didier; Cao, Zhen; Chawla, Mohit; Cavallo, Luigi; Oliva, Romina; Yin, Rui; Cheung, Melyssa; Guest, Johnathan D.; Lee, Jessica; Pierce, Brian G.; Shor, Ben; Cohen, Tomer; Halfon, Matan; Schneidman-Duhovny, Dina; Zhu, Shaowen; Yin, Rujie; Sun, Yuanfei; Shen, Yang; Maszota-Zieleniak, Martyna; Bojarski, Krzysztof K.; Lubecka, Emilia A.; Marcisz, Mateusz; Danielsson, Annemarie; Dziadek, Lukasz; Gaardlos, Margrethe; Gieldon, Artur; Liwo, Adam; Samsonov, Sergey A.; Slusarz, Rafal; Zieba, Karolina; Sieradzan, Adam K.; Czaplewski, Cezary; Kobayashi, Shinpei; Miyakawa, Yuta; Kiyota, Yasuomi; Takeda-Shitaka, Mayuko; Olechnovič, Kliment; Valančauskas, Lukas; Dapkūnas, Justas; Venclovas, Česlovas; Wallner, Bjorn; Yang, Lin; Hou, Chengyu; He, Xiaodong; Guo, Shuai; Jiang, Shenda; Ma, Xiaoliang; Duan, Rui; Qui, Liming; Xu, Xianjin; Zou, Xiaoqin; Velankar, Sameer; Wodak, Shoshana J. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment // Proteins: structure, function and bioinformatics: Special Issue: CASP15: Critical Assessment of methods for Structure Prediction, 15th round. Hoboken : John Wiley and Sons Inc. ISSN 0887-3585. eISSN 1097-0134. 2023, vol. 91, iss. 12, p. 1658-1683. DOI: 10.1002/prot.26609. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 3.200; AIF: 4.400; Q2 (2023 InCities JCR SCIE)]

2022
1 Petraitytė, Gunda; Mikštienė, Violeta; Siavrienė, Evelina; Cimbalistienė, Loreta; Maldžienė, Živilė; Rančelis, Tautvydas; Vaitėnienė, Evelina Marija; Ambrozaitytė, Laima; Dapkūnas, Justas; Dzindzalieta, Ramūnas; Pranckevičienė, Erinija; Kučinskas, Vaidutis; Utkus, Algirdas; Preikšaitienė, Eglė. Donor splice site variant in SLC9A6 causes Christianson syndrome in a Lithuanian family: a case report // Medicina. Kaunas; Basel : LSMU ; MDPI AG. ISSN 1010-660X. eISSN 1648-9144. 2022, vol. 58, no. 3, art. no. 351, p. [1-11]. DOI: 10.3390/medicina58030351. [DB: Science Citation Index Expanded (Web of Science), Scopus, MEDLINE] [IF: 2.600; AIF: 6.700; Q3 (2022 InCities JCR SCIE)]
2 Siavrienė, Evelina; Maldžienė, Živilė; Mikštienė, Violeta; Petraitytė, Gunda; Rančelis, Tautvydas; Dapkūnas, Justas; Burnytė, Birutė; Benušienė, Eglė; Sasnauskienė, Aušra; Grikinienė, Jurgita; Griškevičiūtė, Eglė; Utkus, Algirdas; Preikšaitienė, Eglė. PIGN-related disease in two Lithuanian families: a report of two novel pathogenic variants, molecular and clinical characterisation // Medicina. Basel : LSMU ; MDPI. ISSN 1010-660X. eISSN 1648-9144. 2022, vol. 58, no. 11, art. no. 1526, p. [1-13]. DOI: 10.3390/medicina58111526. [DB: Science Citation Index Expanded (Web of Science), Scopus] [IF: 2.600; AIF: 6.700; Q3 (2022 InCities JCR SCIE)]

2021
1 Dapkūnas, Justas; Olechnovič, Kliment; Venclovas, Česlovas. Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction // Proteins: structure, function, and bioinformatics: Special Issue: CASP14: Critical Assessment of methods of protein Structure Prediction, 14th round. Hoboken : Wiley. ISSN 0887-3585. eISSN 1097-0134. 2021, vol. 89, iss. 12, p. 1834-1843. DOI: 10.1002/prot.26167. [DB: Science Citation Index Expanded (Web of Science), Scopus, BIOSIS Previews, MEDLINE, INSPEC] [IF: 4.088; AIF: 5.561; Q2 (2021 InCities JCR SCIE)]
2 Lensink, Marc F; Brysbaert, Guillaume; Mauri, Théo; Nadzirin, Nurul; Velankar, Sameer; Chaleil, Raphael A G; Clarence, Tereza; Bates, Paul A; Kong, Ren; Liu, Bin; Yang, Guangbo; Liu, Ming; Shi, Hang; Lu, Xufeng; Chang, Shan; Roy, Raj S; Quadir, Farhan; Liu, Jian; Cheng, Jianlin; Antoniak, Anna; Czaplewski, Cezary; Giełdoń, Artur; Kogut, Mateusz; Lipska, Agnieszka G; Liwo, Adam; Lubecka, Emilia A; Maszota-Zieleniak, Martyna; Sieradzan, Adam K; Ślusarz, Rafał; Wesołowski, Patryk A; Zięba, Karolina; Del Carpio Muñoz, Carlos A; Ichiishi, Eiichiro; Harmalkar, Ameya; Gray, Jeffrey J; Bonvin, Alexandre M J J; Ambrosetti, Francesco; Vargas Honorato, Rodrigo; Jandova, Zuzana; Jiménez-García, Brian; Koukos, Panagiotis I; Van Keulen, Siri; Van Noort, Charlotte W; Réau, Manon; Roel-Touris, Jorge; Kotelnikov, Sergei; Padhorny, Dzmitry; Porter, Kathryn A; Alekseenko, Andrey; Ignatov, Mikhail; Desta, Israel; Ashizawa, Ryota; Sun, Zhuyezi; Ghani, Usman; Hashemi, Nasser; Vajda, Sandor; Kozakov, Dima; Rosell, Mireia; Rodríguez-Lumbreras, Luis A; Fernandez-Recio, Juan; Karczynska, Agnieszka; Grudinin, Sergei; Yan, Yumeng; Li, Hao; Lin, Peicong; Huang, Sheng-You; Christoffer, Charles; Terashi, Genki; Verburgt, Jacob; Sarkar, Daipayan; Aderinwale, Tunde; Wang, Xiao; Kihara, Daisuke; Nakamura, Tsukasa; Hanazono, Yuya; Gowthaman, Ragul; Guest, Johnathan D; Yin, Rui; Taherzadeh, Ghazaleh; Pierce, Brian G; Barradas-Bautista, Didier; Cao, Zhen; Cavallo, Luigi; Oliva, Romina; Sun, Yuanfei; Zhu, Shaowen; Shen, Yang; Park, Taeyong; Woo, Hyeonuk; Yang, Jinsol; Kwon, Sohee; Won, Jonghun; Seok, Chaok; Kiyota, Yasuomi; Kobayashi, Shinpei; Harada, Yoshiki; Takeda-Shitaka, Mayuko; Kundrotas, Petras J; Singh, Amar; Vakser, Ilya A; Dapkūnas, Justas; Olechnovič, Kliment; Venclovas, Česlovas; Duan, Rui; Qiu, Liming; Xu, Xianjin; Zhang, Shuang; Zou, Xiaoqin; Wodak, Shoshana J. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment // Proteins: structure, function, and bioinformatics: Special Issue: CASP14: Critical Assessment of methods of protein Structure Prediction, 14th round. Hoboken : Wiley. ISSN 0887-3585. eISSN 1097-0134. 2021, vol. 89, iss. 12, p. 1800-1823. DOI: 10.1002/prot.26222. [DB: Science Citation Index Expanded (Web of Science), Scopus, BIOSIS Previews, MEDLINE, INSPEC] [IF: 4.088; AIF: 5.561; Q2 (2021 InCities JCR SCIE)]
3 Dapkūnas, Justas; Timinskas, Albertas; Olechnovič, Kliment; Tomkuvienė, Miglė; Venclovas, Česlovas. PPI3D: a computational resource for searching, analysis and modeling protein-protein, protein-peptide and protein-nucleic acid interactions // Protein science: Award Winners and Abstracts of the 35th Anniversary Symposium of The Protein Society, July 7–14, 2021 | Virtual. Hoboken : Wiley. ISSN 0961-8368. eISSN 1469-896X. 2021, vol. 30, suppl. 1, art. no. 507, p. 189. DOI: 10.1002/pro.4191. [DB: Science Citation Index Expanded (Web of Science)] [IF: 6.993; AIF: 6.490; Q1 (2021 InCities JCR SCIE)]

2020
1 Dapkūnas, Justas; Kairys, Visvaldas; Olechnovič, Kliment; Venclovas, Česlovas. Template-based modeling of diverse protein interactions in CAPRI rounds 38-45 // Proteins: structure, function and bioinformatics. Hoboken : John Wiley and Sons Inc. ISSN 0887-3585. eISSN 1097-0134. 2020, vol. 88, no. 8, p. 939-947. DOI: 10.1002/prot.25845. [DB: Scopus, Science Citation Index Expanded (Web of Science)] [IF: 3.756; AIF: 5.051; Q2 (2020 InCities JCR SCIE)]
2 Dapkūnas, Justas; Venclovas, Česlovas. Template-based modeling of protein complexes using the PPI3D web server // Protein structure prediction / ed.: Daisuke Kihara. New York : Humana Press; Springer Science+Business Media, 2020. ISBN 9781071607077. eISBN 9781071607084. p. 139-155. (Methods in molecular biology, ISSN 1064-3745, eISSN 1940-6029 ; vol. 2165). DOI: 10.1007/978-1-0716-0708-4_8. [DB: Book Citation Index - Science (Web of Science), Scopus, SpringerLink]
3 Kučinskaitė-Kodzė, Indrė; Simanavičius, Martynas; Dapkūnas, Justas; Plečkaitytė, Milda; Žvirblienė, Aurelija. Mapping of recognition sites of monoclonal antibodies responsible for the inhibition of pneumolysin functional activity // Biomolecules. Basel : MDPI AG. eISSN 2218-273X. 2020, vol. 10, iss. 7, art. no. 1009, p. [1-19]. DOI: 10.3390/biom10071009. [DB: Embase, BIOSIS Previews, MEDLINE, Science Citation Index Expanded (Web of Science), Scopus]

2019
1 Jankauskaitė, Justina; Jiménez-García, Brian; Dapkūnas, Justas; Fernandez-Recio, Juan; Moal, Iain H. SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation // Bioinformatics. London : Oxford University Press. ISSN 1367-4803. eISSN 1460-2059. 2019, vol. 35, iss. 3, p. 462-469. DOI: 10.1093/bioinformatics/bty635. [DB: Embase, Current Contents, BIOSIS Previews, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 5.610; AIF: 3.547; Q1 (2019 InCities JCR SCIE)]
2 Grigaitis, Pranas; Jonušienė, Violeta; Žitkutė, Vilmantė; Dapkūnas, Justas; Dabkevičienė, Daiva; Sasnauskienė, Aušra. Exogenous interleukin-1α signaling negatively impacts acquired chemoresistance and alters cell adhesion molecule expression pattern in colorectal carcinoma cells HCT116. // Cytokine. Oxford : Elsevier science. ISSN 1043-4666. eISSN 1096-0023. 2019, vol. 114, p. 38-46. DOI: 10.1016/j.cyto.2018.11.031. [DB: MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.952; AIF: 5.187; Q3 (2019 InCities JCR SCIE)]
3 Lensink, Marc F; Brysbaert, Guillaume; Nadzirin, Nurul; Velankar, Sameer; Chaleil, Raphaël A G; Gerguri, Tereza; Bates, Paul A; Laine, Elodie; Carbone, Alessandra; Grudinin, Sergei; Kong, Ren; Liu, Ran-Ran; Xu, Xi-Ming; Shi, Hang; Chang, Shan; Eisenstein, Miriam; Karczynska, Agnieszka; Czaplewski, Cezary; Lubecka, Emilia; Lipska, Agnieszka; Krupa, Paweł; Mozolewska, Magdalena; Golon, Łukasz; Samsonov, Sergey; Liwo, Adam; Crivelli, Silvia; Pagès, Guillaume; Karasikov, Mikhail; Kadukova, Maria; Yan, Yumeng; Huang, Sheng-You; Rosell, Mireia; Rodríguez-Lumbreras, Luis A; Romero-Durana, Miguel; Díaz-Bueno, Lucía; Fernandez-Recio, Juan; Christoffer, Charles; Terashi, Genki; Shin, Woong-Hee; Aderinwale, Tunde; Maddhuri Venkata Subraman, Sai Raghavendra; Kihara, Daisuke; Kozakov, Dima; Vajda, Sandor; Porter, Kathryn; Padhorny, Dzmitry; Desta, Israel; Beglov, Dmitri; Ignatov, Mikhail; Kotelnikov, Sergey; Moal, Iain H; Ritchie, David W; Chauvot de Beauchêne, Isaure; Maigret, Bernard; Devignes, Marie-Dominique; Ruiz Echartea, Maria E; Barradas-Bautista, Didier; Cao, Zhen; Cavallo, Luigi; Oliva, Romina; Cao, Yue; Shen, Yang; Baek, Minkyung; Park, Taeyong; Woo, Hyeonuk; Seok, Chaok; Braitbard, Merav; Bitton, Lirane; Scheidman-Duhovny, Dina; Dapkūnas, Justas; Olechnovič, Kliment; Venclovas, Česlovas; Kundrotas, Petras J; Belkin, Saveliy; Chakravarty, Devlina; Badal, Varsha D; Vakser, Ilya A; Vreven, Thom; Vangaveti, Sweta; Borrman, Tyler; Weng, Zhiping; Guest, Johnathan D; Gowthaman, Ragul; Pierce, Brian G; Xu, Xianjin; Duan, Rui; Qiu, Liming; Hou, Jie; Ryan Merideth, Benjamin; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Koukos, Panos I; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jörg; Trellet, Mikael E; Melquiond, Adrien S J; Xue, Li; Jiménez-García, Brian; van Noort, Charlotte W; Honorato, Rodrigo V; Bonvin, Alexandre M J J; Wodak, Shoshana J. Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment // Proteins: structure, function, and bioinformatics. Hoboken : Wiley Periodicals, Inc. ISSN 0887-3585. eISSN 1097-0134. 2019, vol. 87, iss. 12, p. 1200-1221. DOI: 10.1002/prot.25838. [DB: MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.828; AIF: 4.180; Q2 (2019 InCities JCR SCIE)]
4 Dapkūnas, Justas; Olechnovič, Kliment; Venclovas, Česlovas. Structural modeling of protein complexes: Current capabilities and challenges // Proteins: structure, function and bioinformatics: Special issue: Critical assessment of methods of protein structure prediction. Hoboken : John Wiley and Sons Inc. ISSN 0887-3585. eISSN 1097-0134. 2019, vol. 87, iss. 12, p. 1222-1232. DOI: 10.1002/prot.25774. [DB: Biological Abstracts, Biobase, Current Contents, MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.828; AIF: 4.180; Q2 (2019 InCities JCR SCIE)]

2018
1 Dapkūnas, Justas; Olechnovič, Kliment; Venclovas, Česlovas. Modeling of protein complexes in CAPRI Round 37 using template-based approach combined with model selection // Proteins: structure, function, and bioinformatics. Hoboken : Wiley Periodicals, Inc. ISSN 0887-3585. eISSN 1097-0134. 2018, vol. 86, iss. S 1, p. 292-301. DOI: 10.1002/prot.25378. [DB: MEDLINE, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.501; AIF: 3.989; Q3 (2018 InCities JCR SCIE)]

2017
1 Dapkūnas, Justas; Timinskas, Albertas; Olechnovič, Kliment; Margelevičius, Mindaugas; Dičiūnas, Rytis; Venclovas, Česlovas. The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures // Bioinformatics. Oxford : Oxford University Press. ISSN 1367-4803. eISSN 1460-2059. 2017, Vol. 33, Iss. 6, p. 935-937. DOI: 10.1093/bioinformatics/btw756. [DB: MEDLINE, Chemical abstracts, BIOSIS Previews, Biological Abstracts, Science Citation Index Expanded (Web of Science)] [IF: 5.481; AIF: 3.141; Q1 (2017 InCities JCR SCIE)]

2015
1 Moal, Iain H.; Dapkūnas, Justas; Fernandez-Recio, Juan. Inferring the microscopic surface energy of protein–protein interfaces from mutation data // Proteins: structure, function, and bioinformatics. Hoboken : Wiley Periodicals, Inc. ISSN 0887-3585. eISSN 1097-0134. 2015, Vol. 83, no 4, p. 640-650. DOI: 10.1002/prot.24761. [DB: Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.499; AIF: 3.674; Q2 (2015 InCities JCR SCIE)]

2014
1 Dapkūnas, Justas; Timinskas, Albertas; Olechnovič, Kliment; Margelevičius, Mindaugas; Dičiūnas, Rytis; Venclovas, Česlovas. The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures // 50th anniversary of FEBS : Abstracts book of The XIIIth International Conference of Lithuanian Biochemical Society, June 18-20, 2014. Vilnius. 2014, p. 17. Prieiga per internetą: <http://www.elib.grsu.by/katalog/481236pdf.pdf?d=true> [žiūrėta 2016-05-16].

2011
1 Lanevskij, Kiril; Dapkūnas, Justas; Juška, Liutauras; Japertas, Pranas; Didžiapetris, Remigijus. QSAR analysis of blood–brain distribution: The influence of plasma and brain tissue binding // Journal of pharmaceutical sciences. Hoboken : John Wiley & Sons, Inc. ISSN 0022-3549. 2011, Vol. 100, no. 6, p. 2147-2160. DOI: 10.1002/jps.22442. [DB: Science Citation Index Expanded (Web of Science), BIOSIS Previews, Chemical abstracts, CABI Abstracts Databases, Scopus, MEDLINE] [IF: 3.055; AIF: 3.481; Q2 (2011 InCities JCR SCIE)]

2010
1 Didžiapetris, Remigijus; Dapkūnas, Justas; Sazonovas, Andrius; Japertas, Pranas. Trainable structure–activity relationship model for virtual screening of CYP3A4 inhibition // Journal of computer-aided molecular design. Dordrecht : Springer. ISSN 0920-654X. 2010, Vol. 24, no. 11, p. 891-906. DOI: 10.1007/s10822-010-9381-1. [DB: MEDLINE, Chemical abstracts, BIOSIS Previews, Science Citation Index Expanded (Web of Science)] [IF: 3.374; AIF: 3.087; Q1 (2010 InCities JCR SCIE)]

2009
1 Dapkūnas, Justas; Sazonovas, Andrius; Japertas, Pranas. Probabilistic prediction of the human CYP3A4 and CYP2D6 metabolism sites // Chemistry & biodiversity. Weinheim : Wiley-V C H Verlag GMBH. ISSN 1612-1872. 2009, Vol. 6, iss. 11, p. 2101-2106. DOI: 10.1002/cbdv.200900078. [DB: Science Citation Index Expanded (Web of Science), Chemical abstracts, MEDLINE, CABI Abstracts Databases, Elsevier Biobase, Scopus, Embase] [IF: 1.926; AIF: 4.068; Q2 (2009 InCities JCR SCIE)]