Dr. Kliment Olechnovič

Updated on 2024-02-06.
Latest CV online: https://www.kliment.lt | pdf.

General information

Occupation
MSCA Postdoctoral Fellow at CNRS Laboratoire Jean Kuntzmann, Grenoble, France (from 2023-09-01 to 2025-08-31)
on sabbatical leave as Senior Researcher at Vilnius University Life Sciences Center until 2025-09-01
Email

Online profiles

Google Scholar
https://scholar.google.lt/citations?user=uT_t5ewAAAAJ
ORCID
https://orcid.org/0000-0003-4918-9505
GitHub
https://github.com/kliment-olechnovic

Main research interests

Education

2012–2017
Ph.D. Computer Science, Vilnius University
2010–2012
M.S. Computer Science, Vilnius University (Magna Cum Laude)
2005–2009
B.S. Bioinformatics, Vilnius University

Work experience

2023–now
MSCA Postdoctoral Fellow (CNRS Laboratoire Jean Kuntzmann, Grenoble, France)
2020–2023
Senior Researcher (Vilnius University / Life Sciences Center / Institute of Biotechnology)
2021–2023
Visiting researcher, for 28 weeks in total (CNRS Laboratoire Jean Kuntzmann, Grenoble, France)
2017–2020
Researcher (Vilnius University / Life Sciences Center / Institute of Biotechnology)
2019–2020
Visiting researcher, for 9 weeks (Inria, Grenoble, France)
2013–2017
Junior Researcher (Vilnius University / Institute of Biotechnology)
2010–2013
Research Engineer (Vilnius University / Institute of Biotechnology)
2009–2010
Research Engineer (Institute of Biotechnology, Vilnius)
2007–2008
C++ software developer (4Team Corporation, Vilnius)

Publications

Research papers

  1. (preprint) Voronota-LT: efficient, flexible and solvent-aware tessellation-based analysis of atomic interactions.
    Olechnovič K, Grudinin S.
    Preprint in bioRxiv. 2024.
    doi:10.1101/2024.02.05.577169.

  2. VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network.
    Olechnovič K, Venclovas Č.
    Proteins. 2023 Jul 21.
    doi:10.1002/prot.26554.
    PMID:37482904.

  3. Prediction of protein assemblies by structure sampling followed by interface-focused scoring.
    Olechnovič K, Valančauskas L, Dapkūnas J, Venclovas Č.
    Proteins. 2023 Aug 14.
    doi:10.1002/prot.26569.
    PMID:37578163.

  4. (preprint) TemStaPro: protein thermostability prediction using sequence representations from protein language models.
    Pudžiuvelytė I, Olechnovič K, Godliauskaite E, Sermokas K, Urbaitis T, Gasiunas G, Kazlauskas D.
    Preprint in bioRxiv. 2023.
    doi:10.1101/2023.03.27.534365.

  5. Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment.
    Lensink M, Brysbaert G, Raouraoua N, Bates P, Giulini M, Vargas Honorato R, van Noort C, Teixeira J, MJJ Bonvin A, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy R, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio C, Ichiishi E, Fernández-Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray J, Li H, Lin P, He J, Tao H, Huang S, Roel J, Jimenez-Garcia B, Christoffer C, Jain A, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt J, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi S, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest J, Lee J, Pierce B, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski K, Lubecka E, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Giełdoń A, Liwo J, Samsonov S, Slusarz R, Zieba K, Sieradzan A, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovič K, Valančauskas L, Dapkūnas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qiu L, Xu X, Zou X, Velankar S, Wodak S.
    Proteins. 2023 Oct 31.
    doi:10.1002/prot.26609.
    PMID:37905971.

  6. Discriminating Physiological from Non-Physiological Interfaces in Structures of Protein Complexes: A Community-Wide Study.
    Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LÁ, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin A, Savojardo C, Martelli P-L, Casadio R, Tubiana J, Wolfson H, Oliva R, Barradas-Bautista D, Ricciardelli T, Cavallo L, Venclovas Č, Olechnovič K, Guerois R, Andreani J, Martin J, Wang X, Kihara D, Marchand A, Correia B, Zou X, Dey S, Dunbrack R, Levy E, Wodak S.
    Proteomics. 2023 Jun 27.
    doi:10.1002/pmic.202200323.
    PMID:37365936.

  7. Modeling SARS-CoV2 proteins in the CASP-commons experiment.
    Kryshtafovych A, Moult A, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas Č, Won J, et al.
    Proteins. 2021 Aug 30.
    doi:10.1002/prot.26231.
    PMID:34462960.

  8. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
    Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, GiełdoŃ A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, ZiĘba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Honorato RV, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Zhang S, Zou X, Wodak SJ.
    Proteins. 2021 Aug 28.
    doi:10.1002/prot.26222.
    PMID:34453465.

  9. Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction.
    Dapkūnas J, Olechnovič K, Venclovas Č.
    Proteins. 2021 Jun 27.
    doi:10.1002/prot.26167.
    PMID:34176161.

  10. VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures.
    Olechnovič K, Venclovas Č.
    Bioinformatics. 2021 Jun 16. pdf.
    doi:10.1093/bioinformatics/btab448.
    PMID:34132767.

  11. VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures.
    Igashov I, Olechnovič K, Kadukova M, Venclovas Č, Grudinin S.
    Bioinformatics. 2021 Feb 23.
    doi:10.1093/bioinformatics/btab118.
    PMID:33620450.

  12. Template-based modeling of diverse protein interactions in CAPRI rounds 38-45.
    Dapkūnas J, Kairys V, Olechnovič K, Venclovas Č.
    Proteins. 2020 Aug;88(8):939-947. pdf.
    doi:10.1002/prot.25845.
    PMID:31697420.

  13. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
    Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang SY, Rosell M, Rodríguez-Lumbreras LA, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subraman SR, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, Chauvot de Beauchêne I, Maigret B, Devignes MD, Ruiz Echartea ME, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, Dapkūnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, Weng Z, Guest JD, Gowthaman R, Pierce BG, Xu X, Duan R, Qiu L, Hou J, Ryan Merideth B, Ma Z, Cheng J, Zou X, Koukos PI, Roel-Touris J, Ambrosetti F, Geng C, Schaarschmidt J, Trellet ME, Melquiond ASJ, Xue L, Jiménez-García B, van Noort CW, Honorato RV, Bonvin AMJJ, Wodak SJ.
    Proteins. 2019 Dec;87(12):1200-1221.
    doi:10.1002/prot.25838.
    PMID:31612567.

  14. Structural modeling of protein complexes: Current capabilities and challenges.
    Dapkūnas J, Olechnovič K, Venclovas Č.
    Proteins. 2019 Dec;87(12):1222-1232.
    doi:10.1002/prot.25774.
    PMID:31294859.

  15. Estimation of model accuracy in CASP13.
    Cheng J, Choe MH, Elofsson A, Han KS, Hou J, Maghrabi AHA, McGuffin LJ, Menéndez-Hurtado D, Olechnovič K, Schwede T, Studer G, Uziela K, Venclovas Č, Wallner B.
    Proteins. 2019 Dec;87(12):1361-1377.
    doi:10.1002/prot.25767.
    PMID:31265154.

  16. VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes.
    Olechnovič K, Venclovas Č.
    Nucleic Acids Res. 2019 Jul 2;47(W1):W437-W442.
    doi:10.1093/nar/gkz367.
    PMID:31073605.

  17. Comparative analysis of methods for evaluation of protein models against native structures.
    Olechnovič K, Monastyrskyy B, Kryshtafovych A, Venclovas Č.
    Bioinformatics. 2019 Mar 15;35(6):937-944.
    doi:10.1093/bioinformatics/bty760.
    PMID:30169622.

  18. Modeling of protein complexes in CAPRI Round 37 using template-based approach combined with model selection.
    Dapkūnas J, Olechnovič K, Venclovas Č.
    Proteins. 2018 Mar;86 Suppl 1:292-301.
    doi:10.1002/prot.25378.
    PMID:28905467.

  19. VoroMQA: Assessment of protein structure quality using interatomic contact areas.
    Olechnovič K, Venclovas Č.
    Proteins. 2017 Jun;85(6):1131-1145.
    doi:10.1002/prot.25278.
    PMID:28263393.

  20. The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures.
    Dapkūnas J, Timinskas A, Olechnovič K, Margelevičius M, Diciunas R, Venclovas Č.
    Bioinformatics. 2017 Mar 15;33(6):935-937.
    doi:10.1093/bioinformatics/btw756.
    PMID:28011769.

  21. The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.
    Olechnovič K, Venclovas Č.
    Nucleic Acids Res. 2014 Jul;42(Web Server issue):W259-63.
    doi:10.1093/nar/gku294.
    PMID:24838571.

  22. The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures.
    Olechnovič K, Venclovas Č.
    Nucleic Acids Res. 2014 May;42(9):5407-15.
    doi:10.1093/nar/gku191.
    PMID:24623815.

  23. Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls.
    Olechnovič K, Venclovas Č.
    J Comput Chem. 2014 Mar 30;35(8):672-81.
    doi:10.1002/jcc.23538.
    PMID:24523197.

  24. CAD-score: a new contact area difference-based function for evaluation of protein structural models.
    Olechnovič K, Kulberkytė E, Venclovas Č.
    Proteins. 2013 Jan;81(1):149-62.
    doi:10.1002/prot.24172.
    PMID:22933340.

  25. Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure.
    Olechnovič K, Margelevičius M, Venclovas Č.
    Bioinformatics. 2011 Mar 1;27(5):723-4.
    doi:10.1093/bioinformatics/btq720.
    PMID:21186248.

Book chapters

Doctoral dissertation

Other publications

Presentations and posters

Oral presentations at international conferences

Poster presentations at international conferences

Gallery of posters: www.kliment.lt/posters

Main published software

Achievements and awards

Achievements in CASP and CAPRI experiments

CASP (Critical Assessment of Techniques for Protein Structure Prediction) and CAPRI (Critical Assessment of PRedicted Interactions) are world-wide experiments focused on the blind testing of methods for protein structural bioinformatics.

2022
Contributed to one of the top performances in modeling structures of protein complexes in CASP15 and CASP15-CAPRI experiments (ranked 2nd in CASP, ranked 1st in CAPRI). Group “Venclovas”, members: Olechnovič K, Valančauskas L, Dapkūnas J, Venclovas Č.
2022
One of the top performances in EMA (estimation of model accuracy) in CASP15 experiment (and ranked 1st in CASP15-CAPRI scoring experiment). Groups “Venclovas” and “VoroIF”.
2020
Contributed to one of the top performances in modeling structures of protein complexes in CASP14 and CASP14-CAPRI experiments (ranked 2nd in CASP, ranked 1st in CAPRI jointly with two other groups). Group “Venclovas”, members: Olechnovič K, Dapkūnas J, Venclovas Č.
2019
Contributed to one of the top performances (ranked 3rd) in modeling structures of protein complexes in the CAPRI experiment rounds 38–45. Group “Venclovas”, members: Dapkūnas J, Kairys V, Olechnovič K, Venclovas Č.
2018
Contributed to the best results (ranked 1st) in modeling structures of protein complexes in CASP13 and CASP13-CAPRI experiments. Group “Venclovas”, members: Dapkūnas J, Olechnovič K, Venclovas Č.
2018
One of the top performances in EMA (estimation of model accuracy) in CASP13 experiment (ranked 1st in prediction of unreliable regions). Groups “VoroMQA-A” and “VoroMQA-B”.
2016
Contributed to the best results (ranked 1st) in modeling structures of protein complexes in CASP12-CAPRI experiment. Group “Venclovas”, members: Dapkūnas J, Olechnovič K, Venclovas Č.
2016
One of the top performances in protein structure prediction in CASP12 experiment. Group “VoroMQA-select”.

National awards

2019
Lithuanian Academy of Sciences scholarship for young scientists
2018
Laureate of the “Best doctoral dissertation of 2017 in Lithuania” contest
2015
Lithuanian Academy of Sciences award for the best works by young researchers in 2014
2013–2014
The Research Council of Lithuania scholarship for PhD students actively conducting scientific research
2013
INFOBALT incentive scholarship for young scientists

Conference awards

2019
ISCB Art in Science Award Winner at “ISMB/ECCB 2019”. Work title: “Disassembled tessellation”.
2016
Poster selected for an oral presentation at “12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12 meeting)”. Poster title: VoroMQA: assessment of protein structure quality using interatomic contact areas derived from the Voronoi tessellation of atomic balls.
2013
Best poster award at “Society for Bioinformatics in Northern European countries (SocBiN)”. Poster title: The use of interatomic contact areas for the assessment of RNA 3D structural models.
2012
Poster selected for an oral presentation at “EMBO Conference on Critical Assessment of Protein Structure Prediction (CASP10 meeting)”. Poster title: CAD-score: a new method for the evaluation of protein structural models.

Other achievements

2018
Judo champion of Lithuania, judo black belt.
2018
Sambo champion of Lithuania.