VU Gyvybės mokslų centro autoriaus 'Andrius Merkys' publikacijų sąrašas

2023
1 Merkys, Andrius; Vaitkus, Antanas; Grybauskas, Algirdas; Konovalovas, Aleksandras; Quirós, Miguel; Gražulis, Saulius. Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions // Journal of cheminformatics. London : BMC. ISSN 1758-2946. 2023, vol. 15, iss. 1, art. no. 25, p. [1-13]. DOI: 10.1186/s13321-023-00692-1. [DB: Science Citation Index Expanded (Web of Science), Scopus]
2 Lingė, Darius; Gedgaudas, Marius; Merkys, Andrius; Petrauskas, Vytautas; Vaitkus, Antanas; Grybauskas, Algirdas; Paketurytė-Latvė, Vaida; Zubrienė, Asta; Zakšauskas, Audrius; Mickevičiūtė, Aurelija; Smirnovienė, Joana; Baranauskienė, Lina; Čapkauskaitė, Edita; Dudutienė, Virginija; Urniežius, Ernestas; Konovalovas, Aleksandras; Kazlauskas, Egidijus; Shubin, Kirill; Schiöth, Helgi B; Chen, Wen-Yih; Ladbury, John E; Gražulis, Saulius; Matulis, Daumantas. PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters // Database : the journal of biological databases and curation. Oxford : Oxford university press. eISSN 1758-0463. 2023, vol. 2023, art. no. baad040, p. [1-8]. DOI: 10.1093/database/baad040. [DB: Science Citation Index Expanded (Web of Science)]
3 Vaitkus, Antanas; Merkys, Andrius; Sander, Thomas; Quirós, Miguel; Thiessen, Paul A; Bolton, Evan E; Gražulis, Saulius. A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database // Journal of cheminformatics. London : BMC. ISSN 1758-2946. 2023, vol. 15, iss. 1, art. no. 123, p. [1-15]. DOI: 10.1186/s13321-023-00780-2. [DB: Science Citation Index Expanded (Web of Science), Scopus]

2022
1 Petrauskas, Karolis; Merkys, Andrius; Vaitkus, Antanas; Laibinis, Linas; Gražulis, Saulius. Proving the correctness of the algorithm for building a crystallographic space group // Journal of applied crystallography. Chester : International Union of Crystallography. ISSN 0021-8898. eISSN 1600-5767. 2022, vol. 55, no. 3, p. 515-525. DOI: 10.1107/S1600576722003107. [DB: Science Citation Index Expanded (Web of Science), Scopus]
2 Šidlauskaitė, Eglė; Vaitkus, Antanas; Merkys, Andrius. Derivation of a covalent radii table from open crystallographic data // Open readings 2022 : 65th international conference for students of physics and natural sciences, March 15-18, 2022, Vilnius, Lithuania : abstract book. Vilnius : Vilnius University Press, 2022. ISBN 9786090707227. p. 417. Prieiga per internetą: <https://www.openreadings.eu/wp-content/uploads/2022/03/Abstract_book_2022S.pdf>.

2021
1 Andersen, Casper W; Armiento, Rickard; Blokhin, Evgeny; Conduit, Gareth J; Dwaraknath, Shyam; Evans, Matthew L; Fekete, Ádám; Gopakumar, Abhijith; Gražulis, Saulius; Merkys, Andrius; Mohamed, Fawzi; Oses, Corey; Pizzi, Giovanni; Rignanese, Gian-Marco; Scheidgen, Markus; Talirz, Leopold; Toher, Cormac; Winston, Donald; Aversa, Rossella; Choudhary, Kamal; Colinet, Pauline; Curtarolo, Stefano; Di Stefano, Davide; Draxl, Claudia; Er, Suleyman; Esters, Marco; Fornari, Marco; Giantomassi, Matteo; Govoni, Marco; Hautier, Geoffroy; Hegde, Vinay; Horton, Matthew K; Huck, Patrick; Huhs, Georg; Hummelshøj, Jens; Kariryaa, Ankit; Kozinsky, Boris; Kumbhar, Snehal; Liu, Mohan; Marzari, Nicola; Morris, Andrew J; Mostofi, Arash A; Persson, Kristin A; Petretto, Guido; Purcell, Thomas; Ricci, Francesco; Rose, Frisco; Scheffler, Matthias; Speckhard, Daniel; Uhrin, Martin; Vaitkus, Antanas; Villars, Pierre; Waroquiers, David; Wolverton, Chris; Wu, Michael; Yang, Xiaoyu. OPTIMADE, an API for exchanging materials data // Scientific data. Berlin : Nature Publishing Groups. eISSN 2052-4463. 2021, vol. 8, no. 1, art. no. 217, p. [1-10]. DOI: 10.1038/s41597-021-00974-z. [DB: Science Citation Index Expanded (Web of Science), Scopus, MEDLINE]
2 Vaitkus, Antanas; Merkys, Andrius; Gražulis, Saulius. Validation of the crystallography open database using the crystallographic information framework // Journal of applied crystallography. Chester : International Union of Crystallography. ISSN 0021-8898. eISSN 1600-5767. 2021, vol. 54, Pt 2, p. 661-672. DOI: 10.1107/S1600576720016532. [DB: Science Citation Index Expanded (Web of Science), Scopus, Academic Search Premier, INSPEC, Compendex]
3 Vaitkus, Antanas; Merkys, Andrius; Grybauskas, Algirdas; Konovalovas, Aleksandras; Quiros Olozabal, M.; Gražulis, Saulius. Improvements to the data search and validation functionality in the Crystallography Open Database // Acta Crystallographica A-foundation and Advances: Abstracts of the XXV IUCr Congress, Prague, Czech Republic, August 2021. Chester : International Union of Crystallography. ISSN 2053-2733. 2021, vol. 77, suppl. S, art. no. PS-13-8, p. C814. DOI: 10.1107/S010876732108884X. [DB: Science Citation Index Expanded (Web of Science)] [IF: 2.331; AIF: 5.035; Q3 (2021 InCities JCR SCIE)]
4 Šidlauskaitė, Eglė; Merkys, Andrius. Methods for the determination of covalent bonds in small molecule crystals // Open readings 2021 : 64th international conference for students of physics and natural sciences, March 16-29, 2021, Vilnius, Lithuania : abstract book. Vilnius : Vilnius University Press, 2021. ISBN 9786090705902. p. 443. Prieiga per internetą: <https://www.openreadings.eu/wp-content/uploads/2021/03/Abstract_book_2021S.pdf>.

2020
1 Huber, Sebastiaan P; Zoupanos, Spyros; Uhrin, Martin; Talirz, Leopold; Kahle, Leonid; Häuselmann, Rico; Gresch, Dominik; Müller, Tiziano; Yakutovich, Aliaksandr V; Andersen, Casper W; Ramirez, Francisco F; Adorf, Carl S; Gargiulo, Fernando; Kumbhar, Snehal; Passaro, Elsa; Johnston, Conrad; Merkys, Andrius; Cepellotti, Andrea; Mounet, Nicolas; Marzari, Nicola; Kozinsky, Boris; Pizzi, Giovanni. AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance // Scientific data. London : Nature Publishing Groups. eISSN 2052-4463. 2020, vol. 7, art. no. 300, p. [1-18]. DOI: 10.1038/s41597-020-00638-4. [DB: Science Citation Index Expanded (Web of Science), Scopus, MEDLINE]

2019
1 El Mendili, Yassine; Vaitkus, Antanas; Merkys, Andrius; Gražulis, Saulius; Chateigner, Daniel; Mathevet, Fabrice; Gascoin, Stéphanie; Petit, Sebastien; Bardeau, Jean-François; Zanatta, Marco; Secchi, Maria; Mariotto, Gino; Kumar, Arun; Cassetta, Michele; Lutterotti, Luca; Borovin, Evgeny; Orberger, Beate; Simon, Patrick; Hehlen, Bernard; Le Guen, Monique. Raman Open Database: first interconnected Raman–X-ray diffraction open-access resource for material identification // Journal of applied crystallography. Chichester : Wiley-Blackwell Publishing Ltd. ISSN 0021-8898. eISSN 1600-5767. 2019, vol. 52, no. 3, p. 618-625. DOI: 10.1107/S1600576719004229. [DB: Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.995; AIF: 4.200; Q2 (2019 InCities JCR SCIE)]
2 Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Chateigner, Daniel; Lutterotti, Luca; Moeck, Peter; Quiros, Miguel; Downs, Robert T.; Kaminsky, Werner; Le Bail, Armel. Crystallography Open Database: history, development, and perspectives // Materials informatics: methods, tools, and applications / eds.: Olexandr Isayev, Alexander Tropsha, Stefano Curtarolo. Weinheim : Wiley-VCH Verlag GmbH & Co, 2019. ISBN 9783527341214. eISBN 9783527802272. p. 1-39. Prieiga per internetą: <https://media.wiley.com/product_data/excerpt/18/35273412/3527341218-306.pdf> [žiūrėta 2019-11-11].
3 Orberger, Beate; Le Guen, Monique; Thanh, Bui; Kanzari, Aisha; Rodriguez, Celine; Prudhomme, Antoine; Nolte, Harm; Teerlink, Thijs; Koert, Peter; Pilliere, Henry; Lefevre, Thoma; El Mendili, Anas; Delchini, Sylvain; Gražulis, Saulius; Grybauskas, Algirdas; Merkys, Andrius; Vaitkus, Antanas; Borovin, Evgeny; Lutterotti, Luca; Marchand, Emilie. Sonic drilling coupled with on-line-on-mine-analyses: field tests at the Villeveyrac bauxite deposit (Southern France) // Proceedings of 15th SGA Biennial Meeting on Life with Ore Deposits on Earth, University Glasgow, Glasgow, Scotland, August 27-30, 2019, vols 1-4. Geneva : Society for Geology Applied to Mineral Deposits (SGA), 2019. ISBN 9780852619650. p. 1290-1293. [DB: Conference Proceedings Citation Index - Science (Web of Science)]

2018
1 Vaitkus, Antanas; Merkys, Andrius; El Mendili, Yassine; Gražulis, Saulius. The use of interconnected open data for material identification // Open readings 2018: 61st international conference for students of physics and natural sciences, March 20-23, 2018, Vilnius, Lithuania : programme and abstracts. [S.l.] : [s.n.]. 2018, p. 94. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2018/03/book.pdf> [žiūrėta 2018-07-16].
2 Merkys, Andrius; Vaitkus, Antanas; Gražulis, Saulius. Statistical insights into the chemical bonding in crystal structures // Open readings 2018: 61st international conference for students of physics and natural sciences, March 20-23, 2018, Vilnius, Lithuania : programme and abstracts. [S.l.] : [s.n.]. 2018, p. 268. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2018/03/book.pdf> [žiūrėta 2018-08-02].
3 Quirós, Miguel; Gražulis, Saulius; Girdzijauskaitė, Saulė; Merkys, Andrius; Vaitkus, Antanas. Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database // Journal of cheminformatics. London : BioMed Central Ltd. ISSN 1758-2946. 2018, vol. 10, art. no. 23, p. [1-17]. DOI: 10.1186/s13321-018-0279-6. [DB: PubMed, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 4.154; AIF: 3.950; Q1 (2018 InCities JCR SCIE)]
4 Mounet, Nicolas; Gibertini, Marco; Schwaller, Philippe; Campi, Davide; Merkys, Andrius; Marrazzo, Antimo; Sohier, Thibault; Castelli, Ivano Eligio; Cepellotti, Andrea; Pizzi, Giovanni; Marzari, Nicola. Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds // Nature nanotechnology. London : Nature Publishing Group. ISSN 1748-3387. eISSN 1748-3395. 2018, vol. 13, iss. 3, p. 246-252. DOI: 10.1038/s41565-017-0035-5. [DB: MEDLINE, Embase, INSPEC, Academic Search Premier, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 33.407; AIF: 5.873; Q1 (2018 InCities JCR SCIE)]
5 Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas. Crystallography Open Database (COD) // Handbook of materials modeling. Methods: theory and modeling/ Editors: Wanda Andreoni, Sidney Yip. Cham : Springer Nature. 2018, p. 1-19. DOI: 10.1007/978-3-319-42913-7_66-1. [DB: SpringerLink]

2017
1 Merkys, Andrius (tyrėjas); Vaitkus, Antanas (tyrėjas); Butkus, Justas (tyrėjas); Okulič-Kazarinas, Mykolas (tyrėjas); Kairys, Visvaldas (tyrėjas); Gražulis, Saulius (tyrimo ats. vykdytojas). COD::CIF::Parser: an error-correcting CIF parser for the Perl language. Vilnius, 2017. 0. Prieiga per internetą: <https://midas.lt/public-app.html#/research/overview?resourceId=65635&uuid=860f0d79-b509-404a-a72c-1d43ede11c54>.
2 Merkys, Andrius (tyrėjas). Kristalografinių žinių apie mažas molekules panaudojimas makromolekulių struktūrų patikslinimui: atviros mažų molekulių kristalografinės duomenų bazės pritaikymas = Use of prior small molecule crystallographic knowledge for refinement of macromolecular structures: application of the crystallography open database. Vilnius, 2017. 0. Prieiga per internetą: <https://midas.lt/public-app.html#/research/overview?resourceId=71646&uuid=78b833e6-1015-4675-9976-7f78c5b6ba3f>.
3 Okulič-Kazarinas, Mykolas (tyrėjas); Vaitkus, Antanas (tyrėjas); Gražulis, Saulius (tyrimo ats. vykdytojas); Merkys, Andrius (tyrėjas). Stechiometriškai teisingų molekulių atstatymas iš kristalų struktūrų = Computing stoichiometric molecular composition from crystal structures. Vilnius, 2017. 0. Prieiga per internetą: <https://midas.lt/public-app.html#/research/overview?resourceId=71630&uuid=8af78a38-cf68-4c50-8a1e-cbb5f40d2e4f>.
4 Merkys, Andrius (tyrėjas). Statistinių skirstinių mišinių parinkimas vienmačiams duomenims = Fitting of univariate mixture distributions to data using various approaches. Vilnius, 2017. 1 failas. Prieiga per internetą: <https://midas.lt/public-app.html#/research/overview?resourceId=76059&uuid=d9b99023-7d76-4e94-b796-94a9cb858b15>.
5 Merkys, Andrius (tyrėjas). Duomenų įkėlimo įrangos kūrimas atvirai mažų molekulių kristalografinei duomenų bazei COD = Development of the deposition software for small molecule open crystallographic database COD. Vilnius, 2017. 1 failas. Prieiga per internetą: <https://midas.lt/public-app.html#/research/overview?resourceId=76035&uuid=e96fb8fc-5979-4716-9ed3-ef509e838f1b>.
6 Pizzi, Giovanni (tyrėjas); Gražulis, Saulius (tyrėjas); Marzari, Nicola (tyrėjas); Cepellotti, Andrea (tyrėjas); Mounet, Nicolas (tyrėjas); Merkys, Andrius (tyrėjas). A posteriori metaduomenų išgavimas iš automatinio atsekamumo: AiiDA ir TCOD sujungimas = A posteriori metadata from automated provenance tracking: Integration of AiiDA and TCOD. Vilnius, 2017. 1 failas. Prieiga per internetą: <https://midas.lt/public-app.html#/research/overview?resourceId=76044&uuid=55cbbc54-f61d-4524-912e-dbac135c85ea>.
7 Merkys, Andrius; Vaitkus, Antanas; Gražulis, Saulius. Spotting the unusual geometry in crystal structures // Open Readings 2017 : 60th International conference for students of physics and natural sciences, March 14-17, 2017, Vilnius, Lithuania : programme and abstracts. Vilnius : Vilniaus universitetas. ISSN 2029-4425. 2017, p. 51. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2017/03/OR2017_abstracts_book.pdf> [žiūrėta 2017-07-17].
8 Vaitkus, Antanas; Merkys, Andrius; Gražulis, Saulius. Automating the derivation of chemical information from crystallographic data // Open Readings 2017 : 60th International conference for students of physics and natural sciences, March 14-17, 2017, Vilnius, Lithuania : programme and abstracts. Vilnius : Vilniaus universitetas. ISSN 2029-4425. 2017, p. 136. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2017/03/OR2017_abstracts_book.pdf> [žiūrėta 2017-07-19].
9 Long, Fei; Nicholls, Robert A.; Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N. Validation and extraction of molecular-geometry information from small-molecule databases // Acta crystallographica. Section D : structural biology. Chester : International Union of Crystallography. ISSN 2059-7983. 2017, Vol. 73, Part. 2, p. 103-111. DOI: 10.1107/S2059798317000079. [DB: INSPEC, MEDLINE, Current Contents, Chemical abstracts, BIOSIS Previews, Biological Abstracts, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 3.099; AIF: 3.406; Q2 (2017 InCities JCR SCIE)]
10 Long, Fei; Nicholls, Robert A.; Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Murshudov, Garib N. AceDRG: a stereochemical description generator for ligands // Acta crystallographica. Section D : structural biology. Chester : International Union of Crystallography. ISSN 2059-7983. 2017, Vol. 73, Part 2, p. 112-122. DOI: 10.1107/S2059798317000067. [DB: MEDLINE, INSPEC, Current Contents, Chemical abstracts, BIOSIS Previews, Biological Abstracts, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 3.099; AIF: 3.406; Q2 (2017 InCities JCR SCIE)]
11 Merkys, Andrius; Mounet, Nicolas; Cepellotti, Andrea; Marzari, Nicola; Gražulis, Saulius; Pizzi, Giovanni. A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD // Journal of cheminformatics. London : BioMed Central Ltd. ISSN 1758-2946. 2017, Vol. 9, art. no. 56, [11 p.]. DOI: 10.1186/s13321-017-0242-y. [DB: Zetoc, PubMed Central, PubMed, Scopus, Science Citation Index Expanded (Web of Science)] [IF: 3.893; AIF: 3.549; Q1 (2017 InCities JCR SCIE)]

2016
1 Merkys, Andrius; Vaitkus, Antanas; Butkus, Justas; Okulič-Kazarinas, Mykolas; Kairys, Visvaldas; Gražulis, Saulius. COD::CIF::Parser: an error-correcting CIF parser for the Perl language // Journal of Applied Crystallography. Hoboken : Wiley-Blackwell Publishing Ltd. ISSN 0021-8898. eISSN 1600-5767. 2016, Vol. 49, Part 1, p. 292-301. DOI: 10.1107/S1600576715022396. [DB: Scopus, Chemical abstracts, Science Citation Index Expanded (Web of Science)] [IF: 2.614; AIF: 3.979; Q2 (2016 InCities JCR SCIE)]
2 Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas; Gražulis, Saulius. Spotting the geometric properties in the crystallography open database // Open readings 2016 : 59th scientific conference for students of physics and natural sciences : programme and abstracts. Vilnius : Vilniaus universiteto leidykla. ISSN 2029-4425. 2016, p. 41. Prieiga per internetą: <http://www.openreadings.eu/wp-content/uploads/2016/03/OR2016_abstract_book.pdf> [žiūrėta 2016-10-10].

2015
1 Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas. Computing stoichiometric molecular composition from crystal structures // Journal of Applied Crystallography. Hoboken : Wiley-Blackwell Publishing Ltd. ISSN 0021-8898. eISSN 1600-5767. 2015, Vol. 48, Iss. 1, p. 85-91. DOI: 10.1107/S1600576714025904. [DB: Scopus, Science Citation Index Expanded (Web of Science)] [IF: 2.570; AIF: 3.903; Q2 (2015 InCities JCR SCIE)]

2014
1 Merkys, Andrius; Matusevičiūtė, Agnė; Vaitkus, Antanas; Le Bail, A.; Chateigner, D.; Lutterotti, L.; Quirós-Olozábal, M.; Okulič-Kazarinas, Mykolas; Moeck, P.; Murray-Rust, P.; Downs, R.; Gražulis, Saulius. Chemical information presentation in the Crystallography Open Database // Acta Crystallographica Section A: Foundations and Advances : Abstracts of the XXIII IUCr Congress, Montreal, Canada, 5-12 August 2014 : Abstracts of the XXIII IUCr Congress, Montreal, Canada, 5-12 August 2014. New York : Wiley-Blackwell. ISSN 0108-7673. 2014, Vol. 70, suppl. (August 2014), p. 1710. DOI: 10.1107/S2053273314082898. [DB: ISI Master Journal List, MEDLINE, INSPEC] [IF: 2.325; AIF: 2.280; Q2 (2014 InCities JCR SCIE)]

2012
1 Gražulis, Saulius; Daškevič, Adriana; Merkys, Andrius; Chateigner, Daniel; Lutterotti, Luca; Quiros, Miguel; Serebryanaya, Nadezhda R.; Moeck, Peter; Downs, Robert T.; Bail, Armel Le. Crystallography open database (COD): an open-access collection of crystal structures and platform for world-wide collaboration // Nucleic acids research. Oxford : Oxford University Press. ISSN 0305-1048. 2012, Vol. 40, iss. D1, p. D420-D427. DOI: 10.1093/nar/gkr900. [DB: Science Citation Index Expanded (Web of Science), CAB Abstracts, MEDLINE] [IF: 8.278; AIF: 4.273; Q1 (2012 InCities JCR SCIE)]