Updated on 2024-08-31.
Latest CV online: https://www.kliment.lt
| pdf.
(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.
PPI3D: a web server
for searching, analyzing and modeling protein-protein, protein-peptide
and protein-nucleic acid interactions.
Dapkūnas J, Timinskas A, Olechnovič K, Tomkuvienė M,
Venclovas Č.
Nucleic Acids Res. 2024 Apr.
doi:10.1093/nar/gkae278.
PMID:38619046.
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.
Bioinformatics. 2024 Apr 4.
doi:10.1093/bioinformatics/btae157.
PMID:38507682.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Contact
Area-Based Structural Analysis of Proteins and Their Complexes Using
CAD-Score.
Olechnovič K, Venclovas Č.
In: Zoltán Gáspári (eds) Structural Bioinformatics: Methods and
Protocols, Methods in Molecular Biology, vol. 2112. Springer.
2020.
In Silico
Modeling of Inhibitor Binding to Carbonic Anhydrases.
Kairys V, Olechnovič K, Raškevičius V, Matulis D.
In: Matulis D. (eds) Carbonic Anhydrase as Drug Target.
Springer, Cham. 2019.
Methods for
the analysis and assessment of the three-dimensional structures of
proteins and nucleic acids: development and applications.
Olechnovič K.
Doctoral dissertation, Vilnius University, 2017.
Baltymų ir
nukleorūgščių erdvinių struktūrų analizės ir vertinimo metodai: kūrimas
ir taikymas.
Olechnovič K.
Doctoral dissertation summary in Lithuanian, Vilnius University,
2017.
Kompiuteriai
padeda pažinti sudėtingą baltymų pasaulį.
Dapkūnas J, Olechnovič K.
Popular science article in SPECTRUM. 2017 1(26), ISSN
1822-0147.
Journal cover image
based on the article “VoroMQA: Assessment of protein structure
quality using interatomic contact areas”.
Olechnovič K, Venclovas Č.
Cover Image for Proteins. 2019 Volume 85, Issue 6.
doi:10.1002/prot.25129.
Gallery of posters: www.kliment.lt/posters
Voronota: a standalone software package of various tools for
analyzing three-dimensional structures of biological macromolecules
using the Voronoi diagram of atomic balls (includes the latest versions
of CAD-score and VoroMQA methods).
https://kliment-olechnovic.github.io/voronota
Voronota-JS: an expansion of the core Voronota software. Voronota-JS provides a way to write JavaScript scripts for the comprehensive analysis of macromolecular structures, including the Voronoi tesselation-based analysis. https://kliment-olechnovic.github.io/voronota/expansion_js/
Voronota-LT: an expansion of the core Voronota software. Voronota-LT (pronounced ‘voronota lite’) is an alternative, significantly faster version of Voronota for constructing tessellation-derived atomic contact areas and volumes. https://kliment-olechnovic.github.io/voronota/expansion_lt/
Voronota-GL: a visual tool for the comprehensive interactive analysis of macromolecular structures, including the Voronoi tesselation-based analysis. https://kliment-olechnovic.github.io/voronota/expansion_gl/
FTDMP: a software system for running docking experiments and scoring/ranking multimeric models (includes VoroIF-jury and VoroIF-GNN methods). https://kliment-olechnovic.github.io/ftdmp/
VoroMQA web server for the assessment of protein structure
quality using interatomic contact areas.
https://bioinformatics.lt/wtsam/voromqa
VoroContacts web server for the computation and interactive
querying of Voronoi tessellation-derived contacts.
https://bioinformatics.lt/wtsam/vorocontacts
CAD-score web server for contact area-based comparison of
structures and interfaces of proteins, nucleic acids and their
complexes.
https://bioinformatics.lt/cad-score/
Voroprot: an interactive tool for exploring some
tesselation-derived features of protein structures (no longer
maintained).
https://bioinformatics.lt/software/voroprot
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.
