Our Projects

We were the prime contractor of the scrIN-SILICO project, funded by the European Union.

We participate in the Research University project (2010-2012, TAMOP 4.2.1./B-09/1/KMR-2010-0003), in the Large Systems research area.

Our partners in current projects

Institute of Enzmology, Hungarian Academy of Science, Vertessy lab
Uratim Ltd.
Proteom Services Ltd.

People

Vince Grolmusz
Rafael Ördög
Tamás Rec
Dániel Bánky
Balázs Szerencsi

Former members

Tamás Hubai
Gábor Iván
Annamária Ángyán
Viktor Szabó
Zoltán Szabadka
Elemér Hubenkó
Balázs Kósa

Picture gallery

Publications and Conference Presentations

Árpád Tóth, Dániel Bánky, and Vince Grolmusz: 3D Brownian Motion Simulator for High-Sensitivity Nano-Biotechnological Applications, to appear in IEEE Transactions on Nanobioscience. (Also available as a personal preprint version).

Árpád Tóth, Dániel Bánky, and Vince Grolmusz: Mathematical modeling and computer simulation of Brownian motion and hybridization of nanoparticle-bioprobe-polymer complexes in the low concentration limit, to appear in Molecular Simulation.

Gábor Iván,  Vince Grolmusz: When the Web Meets the Cell: Using Personalized PageRank for Analyzing Protein Interaction Networks,   Bioinformatics Vol. 27, No. 3. pp. 405-407. (also available as a personal preprint version, with additional files).

Gábor Iván, Zoltán Szabadka, Vince Grolmusz: Cysteine and Tryptophan Anomalies Found when Scanning all the Binding Sites in the Protein Data Bank,  (available also as a preliminary version). International Journal of Bioinformatics Research and Applications, Vol. 6, No. 6, 2010, pp. 594-608

Gábor Iván, Vince Grolmusz: Revealing the density-based clustering structure of the SwissProt database (poster) Page 606 of Abstract book, International Congress of Mathematicians 2010 Hyderabad, India, 19th-27th August, 2010

Gábor Iván, Zoltán Szabadka, Vince Grolmusz: A Hybrid Clustering of Protein Binding Sites(preliminary version). FEBS Journal Vol. 277, No. 6. pp. 1494-1502 (2010)

Rafael Ördög, Vince Grolmusz: Frequently appearing spherically aligned substructers in proteins 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA July 11-13, 2010

Gábor Iván, Dániel Bánky, Vince Grolmusz: Refining the protein interaction network generated by NASCENT using sequence alignment 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA July 11-13, 2010

Gábor Iván, Vince Grolmusz: Designing universal oligonucleotides for DNA/nanoparticle conjugates (lecture by Gábor Iván) Nanotech Conference and Expo 2010, Anaheim, California/USA, 21st-25th June, 2010

Árpád Tóth, Dániel Bánky, Vince Grolmusz: Mathematical modeling and computer simulation of Brownian motion and hybridization of nanoparticle-bioprobe-polymer complexes in the low concentration limit Nanotech Conference and Expo 2010, Anaheim, California/USA, 21st-25th June, 2010

Rafael Ördög, Vince Grolmusz: On Delaunay simplices containing functional groups Nanotech Conference and Expo 2010, Anaheim, California/USA, 21st-25th June, 2010

Gábor Iván, Zoltán Szabadka, Vince Grolmusz: On the asymmetry of the residue compositions of the binding sites on protein surfaces;  Journal of Bioinformatics and Computational Biology, Vol. 7. No. 6. (2009) pp. 931-938.

Gábor Iván, Vince Grolmusz: Revealing the density-based clustering structure of the SwissProt database (poster) 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Gábor Iván, Dániel Bánky, Vince Grolmusz: Finding new drug candidates against Mycobacterium tuberculosis using protein-protein interaction networks (poster) 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Gábor Iván, Zoltán Szabadka, Rafael Ördög, Vince Grolmusz: Decomp: a PDB decomposition tool (talk by Gábor Iván) 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) Stockholm, Sweden, 27th June - 2nd July, 2009

Rafael Ördög, Vince Grolmusz: WikiPDB- A community for enhancing the PDB, (talk by Rafael Ördög). 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Dániel Bánky, Rafael Ördög, Vince Grolmusz: NASCENT: An Automatic Protein Interaction Network Generation Tool, (talk by Dániel Bánky). 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Rafael Ördög, Zoltán Szabadka, Vince Grolmusz: DECOMP: A PDB decomposition tool on the web, Bioinformation Vol. 3 No. 10. pp. 413-414 (2009)

Dániel Bánky, Rafael Ördög, Vince Grolmusz: NASCENT: An automatic protein interaction network generation tool for non-model organisms. Bioinformation Vol. 3 No. 8. pp. 361-363 (2009)

Rafael Ördög, Vince Grolmusz: On the bond graphs in the Delaunay-tetrahedra of the simplicial decomposition of spatial protein structures; Proceedings of the International Workshop on Practical Applications of Computational Biology & Bioinformatics (IWPACBB'09) LNCS 5518, University of Salamanca, June 10-12, 2009. Also available as a personal preprint version.

Gábor Iván, Zoltán Szabadka, Rafael Ördög, Vince Grolmusz, Gábor Náray-Szabó: Four Spatial Points That Define Enzyme Families, Biochemical and Biophysical Research Communications, Vol. 383, No. 4, pp. 417-420, (2009) doi:10.1016/j.bbrc.2009.04.022; also available as a personal preprint version.

K. Hill, C.B. Pénzes, B.G. Vértessy, Z. Szabadka, V. Grolmusz, É.Kiss: Amphiphilic Nature of New Antitubercular Drug Candidates and Their Interaction with Lipid Monolayer, Progr Colloid Polym Sci (2008) 135: 87-92, DOI 10.1007/2882_2008_117

Rafael Ördög, Zoltán Szabadka, Vince Grolmusz: A community portal for a better PDB. 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada July 19-July 23, 2008.

Rafael Ördög, Vince Grolmusz: Evaluating Genetic Algorithms in Protein-Ligand Docking , Lecture Notes in Computer Science, Volume 4983/2008, page 402-413

Zoltán Szabadka, Rafael Ördög, Vince Grolmusz: The Ramachandran Map of More Than 6,500 Perfect Polypeptide Chains, Biophysical Reviews and Letters, Vol 2, No. 3 (2007), pp. 1-5

Rafael Ordog, Zoltán Szabadka, Vince Grolmusz: Analyzing the Simplicial Decomposition of Spatial Protein Structures; 6th International Conference on Bioinformatics (InCoB 2007), Hong Kong University of Science and Technology, Hong Kong, 27th-30th August, 2007; Journal version: BMC Bioinformatics, 2008, 9(Suppl 1):S11(doi:10.1186/1471-2105-9-S1-S11), http://www.biomed central.com/1471-2105/9/S1/S11

Zoltán Szabadka, Gábor Iván, Vince Grolmusz: Being a Binding-Site: Characterizing Residue-Composition of Binding Sites on Proteins 6th International Conference on Bioinformatics (InCoB 2007), Hong Kong University of Science and Technology, Hong Kong, 27th-30th August, 2007. Journal version: Bioinformation 2(5), 216-221 (2007), http://www.bio information.net/002/004800022007.htm

Gábor Iván: An Optimized Distance Function for Comparison of Protein Binding Sites, Brazilian Symposium on Bioinformatics (BSB), Angra dos Reis, Brazil, 29th-31th August, 2007, Lecture Notes in Computer Science Volume 4643/2007, pp. 93-100. http://www. springerlink.com/content/k14617662gm623g7/

Gábor Iván:Studying Binding Sites of Protein-Ligand Complexes using Data-Mining Algorithms; SEFI and IGIP Joint Annual Conference, Miskolc, Hungary, 1st-4th July, 2007

Zoltán Szabadka, Gábor Iván, Vince Grolmusz: Analyzing the Residue-Composition of Metal Binding Sites in the Whole Protein Data Bank. Mol. Biol. Cell 17(suppl), 535. (CD-ROM) (Appeared in the Proceedings of the 46th Annual Meeting of the American Society of Cell Biology, December 9-13, 2006, San Diego, CA).

Zoltán Szabadka, Vince Grolmusz:: High Throughput Processing of the Structural Information of the Protein Data Bank, Journal of Molecular Graphics and Modeling, 25 (2007) pp. 831-836 http://dx.doi.org/10 .1016/j.jmgm.2006.08.004

Zoltán Szabadka, Vince Grolmusz: Building a Structured PDB: The RS-PDB Database, Proceedings of the 28th IEEE EMBS Annual International Conference, New York City, Aug. 30-Sept 3, 2006., pp. 5755-5758.

Zoltán Szabadka, Vince Grolmusz: Re-Structuring the PDB , European Conference on Operational Research (EURO 2006) , July 2-5, 2006, Reykjavik, Iceland

Ördög Rafael, Vince Grolmusz: Optimizing the running-structure of genetic-based docking algorithms , 21st European Conference on Operational Research (EURO 2006) , July 2-5, 2006, Reykjavik, Iceland

Zoltán Szabadka, Vince Grolmusz: High Throughput Processing of the Structural Information of the Protein Data Bank DIMACS Workshop on Information Processing by Protein Structures in Molecular Recognition , June 13 - 14, 2005, DIMACS Center, Rutgers University

Balázs Kósa, Zoltán Szabadka, Vince Grolmusz: Mining Protein Binding Sites , European Life Science Organization Meeting (ELSO 2005 ) .

Zoltán Szabadka, Vince Grolmusz: High Throughput Processing of the Structural Information in the Protein Data Bank , European Life Science Organization Meeting (ELSO 2005 ).

Vince Grolmusz, Elemér Hubenkó: Clustering Binding Sites on Protein Surfaces, European Life Science Organization Meeting (ELSO 2005 ).

Last modified: July 5, 2011