2009
Four distances between pairs of amino acids provide a precise description of their interaction
Cohen M, Potapov V, Schreiber G.
The three-dimensional structures of proteins are stabilized by the interactions between amino acid residues. Here we report a method where four distances are calculated between any two side chains to provide an exact spatial definition of their bonds. The data were binned into a four-dimensional...
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
Potapov V, Cohen M, Schreiber G.
Methods for protein modeling and design advanced rapidly in recent years. At the heart of these computational methods is an energy function that calculates the free energy of the system. Many of these functions were also developed to estimate the consequence of mutation on protein stability or...
2008
Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments
Potapov V, Reichmann D, Abramovich R, Filchtinski D, Zohar N, Ben Halevy D, Edelman M, Sobolev V, Schreiber G.
A new method is presented for the redesign of protein-protein interfaces, resulting in specificity of the designed pair while maintaining high affinity. The design is based on modular interface architecture and was carried out on the interaction between TEM1 beta-lactamase and its inhibitor...
2005
The limit of accuracy of protein modeling: influence of crystal packing on protein structure
Eyal E, Gerzon S, Potapov V, Edelman M, Sobolev V.
The size of the protein database (PDB) makes it now feasible to arrive at statistical conclusions regarding structural effects of crystal packing. These effects are relevant for setting upper practical limits of accuracy on protein modeling. Proteins whose crystals have more than one molecule in...
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment
Sobolev V, Eyal E, Gerzon S, Potapov V, Babor M, Prilusky J, Edelman M.
We describe a suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes. LPC/CSU software provides a common definition of inter-atomic contacts and complementarity of contacting surfaces to analyze protein structure and complexes. In the current version of...
2004
Protein-protein recognition: juxtaposition of domain and interface cores in immunoglobulins and other sandwich-like proteins
Potapov V, Sobolev V, Edelman M, Kister A, Gelfand I.
Structural analysis of a non-redundant data set of 47 immunoglobulin (Ig) proteins was carried out using a combination of criteria: atom--atom contact compatibility, position occupancy rate, conservation of residue type and positional conservation in 3D space. Our analysis shows that roughly half...
2003
About factors providing the fast protein-protein recognition in processes of complex formation
Drozdov-Tikhomirov LN, Linde DM, Poroikov VV, Alexandrov AA, Skurida GI, Kovalev PV, Potapov VY.
A package of programs for the examination of areas of subunit contacts (interface) in protein-protein (PP) complexes has been created and used for a detailed study of amino acid (AA) composition and interface structure in a large number of PP complexes from Brookhaven database (PBD). It appeared...
What forces can determine the formation of highly specific protein-protein complexes?
Drozdov-Tikhomirov LN, Linde DM, Poroĭkov VV, Aleksandrov AA, Skurida GI, Kovalev PV, Potapov VY.
A software package was designed and used in a detailed study of the contact regions (interfaces) of a large number of protein-protein complexes using the PDB data. It appeared that for about 75% of the complexes the amino acid composition of the subunit surface in the contact region is not...