This is a list of WEB pages from Edelman-Sobolev Bioinformatics group:
1. LIGIN Program for molecular docking based on surface complementarity.
2. Tools for analysis of Ligand-Protein Contacts (LPC) and Contacts of Structural Units (CSU) in proteins.
3. Tool for structural analysis of point mutations: MutaProt.
4. Vladimir Sobolev's home page.
5. Rafael Najmanovich's home page.

Personnel:
Prof. Meir Edelman, Dr. Vladimir Sobolev - Group heads
Dr. Moshe Van Dyke - PostDoc
Eran Eyal, Mariana Babor and Vladimir Potapov - PhD students
Sergei Gerzon - Scientific programmer

Main Interests:
Modeling cofactor-protein interactions; tools for analyzing molecular structures.

Recent publications:

Sobolev V. and Edelman M. (1995) Modeling the quinone-B site of the photosystem II reaction center using notions of complementarity and contact surface between atoms. Proteins 21, 214-225.

Sobolev V., Wade R.C., Vriend G. and Edelman M. (1996) Molecular docking using surface complementarity. Proteins 25, 120-129.

Sobolev V., Moallem T.M., Wade R.C., Vriend G. and Edelman M. (1997) CASP2 molecular docking predictions with the LIGIN software. Proteins Suppl. 1, 210-214.

Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics 15, 327-332.

Edelman M. and Sobolev V. (1999) Using atomic-level structure to probe protein function. SigBio Newslett. 19, 13-14.

Najmanovich R., Kuttner J., Sobolev V. and Edelman M. (2000) Side chain flexibility in proteins upon ligand binding. Proteins 39, 261-268.

Eyal E., Najmanovich R., Sobolev V. and Edelman M. (2001) MutaProt: a web interface for structural analysis of point mutations. Bioinformatics 17, 381-382.

Kuttner Y.Y., Babor M., Edelman M. and Sobolev V. (2001) Structural commonality in protein binding sites for ATP. in Currents in Computational Molecular Biology 2001 Ed: El-Manrouk N, Lengauer T, Sankoff D.Les Publ.CRM, Montreal; p. 91-92.

McConkey B., Sobolev V. and Edelman M. (2001) Ligand-protein docking using a two stage algorithm: 1. rapid determination of binding site and approximate ligand position. in Currents in Computational Molecular Biology 2001 Ed: El-Manrouk N, Lengauer T, Sankoff D.Les Publ.CRM, Montreal; p. 73-74.

Eyal E., Najmanovich R., Babor M., Edelman M. and Sobolev V. (2001) Protein side-chain flexibility upon point mutations: Deriving the upper limit of predictive accuracy from PDB files. in Currents in Computational Molecular Biology 2001 Ed: El-Manrouk N, Lengauer T, Sankoff D.Les Publ.CRM, Montreal; p. 119-120.

Najmanovich R., Edelman M. and Sobolev V.. (2001) Population boom: an improved genetic algorithm. in Currents in Computational Molecular Biology 2001 Ed: El-Manrouk N, Lengauer T, Sankoff D.Les Publ.CRM, Montreal; p. 139-140.

McConkey B.J., Sobolev V., Edelman M. (2002) The performance of current methods in ligasnd-protein docking. Current Science, 83, 845-856.

McConkey B.J., Sobolev V., and Edelman M. (2002) Quantification of protein surfaces, volumes and atomÄatom contacts using a constrained Voronoi procedure. Bioinformatics 18, 1365-1373.

Sobolev V., Niztaev A., Pick U., Avni A., and Edelman M. (2002) A case study in applying docking predictions: Modeling the tentoxin binding sites of chloroplast F1-ATPase. Current Science, 83, 857-867.

Babor M., Sobolev V., and Edelman M. (2002) Conserved positions for ribos recognition: importance of water bridging interactions among ATP-, ADP- and FAD-protein complexes. J. Mol. Biol. 323, 523-532.

Eyal E, Najmanovich R, Edelman M., and Sobolev V. (2003) Protein side chain rearrangement in regions of point mutations. Proteins, 50, 272-282.

McConkey B.J., Sobolev V. and Edelman M. (2003) Discrimination of native protein structures using atom-atom contact scoring. Proc. Natl. Acad. Sci. USA 100, 3215-3220.

Yakobson E.A., Eisenberg S., Isakson R., Halle D., Levy-Lahad E., Catane R., Safro M., Sobolev V., Huot T., Peters G., Ruiz A., Malvehy J., Puig S., Chompret A., Avril M-F., Shafir R., Peretz H., and Paillerets B.B. (2003) A Single Mediterranean, Possibly Jewish, Origin for the Val59Gly CDKN2A Mutation in Four Melanoma-Prone families. Eur. J. Hum. Gen. 11, 288-296.

Rosenberg N., Yatuv R., Sobolev V., Peretz H., Zivelin A., and Seligsohn U. (2003) Major mutations in CALF-1 and CALF-2 domains of glycoprotein IIB in patients with Glanzmann thrombasthenia enable GPIIB/IIIA complex formation but abolish its transport from the endoplasmic reticulum to the Golgi apparetus. Blood 101, 4808-4815.

Kuttner J., Sobolev V., Raskind A., and Edelman M. (2003) A consensus binding structure for adenine at the atomic level permits searching for the ligand site in a wide spectrum of adenine-containing complexes. Proteins 52, 400-411.


Please mail questions/suggestions concerning this page to vladimir.sobolev@weizmann.ac.il

This page was last modified 1 February 2004