PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. - Mindaugas Margelevicius; Ceslovas Venclovas (BMC Bioinform., 2005)

Re-searcher: a system for recurrent detection of homologous protein sequences. - Valdemaras Repsys; Mindaugas Margelevicius; Ceslovas Venclovas (BMC Bioinform., 2008)

COMA server for protein distant homology search. - Mindaugas Margelevicius; Mindaugas Laganeckas; Ceslovas Venclovas (Bioinform., 2010)

Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison. - Mindaugas Margelevicius; Ceslovas Venclovas (BMC Bioinform., 2010)

Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure. - Kliment Olechnovic; Mindaugas Margelevicius; Ceslovas Venclovas (Bioinform., 2011)

Bayesian nonparametrics in protein remote homology search. - Mindaugas Margelevicius (Bioinform., 2016)

The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures. - Justas Dapkunas; Albertas Timinskas; Kliment Olechnovic; Mindaugas Margelevicius; Rytis Diciunas; Ceslovas Venclovas (Bioinform., 2017)

A low-complexity add-on score for protein remote homology search with COMER. - Mindaugas Margelevicius (Bioinform., 2018)

Estimating statistical significance of local protein profile-profile alignments. - Mindaugas Margelevicius (BMC Bioinform., 2019)

COMER2: GPU-accelerated sensitive and specific homology searches. - Mindaugas Margelevicius (Bioinform., 2020)

The COMER web server for protein analysis by homology. - Justas Dapkunas; Mindaugas Margelevicius (Bioinform., 2023)