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Article ; Online: Prediction of transition metal-binding sites from apo protein structures.

Babor, Mariana / Gerzon, Sergey / Raveh, Barak / Sobolev, Vladimir / Edelman, Marvin

2008 Volume 70, Issue 1, Page(s) 208–217

Abstract: Metal ions are crucial for protein function. They participate in enzyme catalysis, play regulatory roles, and help maintain protein structure. Current tools for predicting metal-protein interactions are based on proteins crystallized with their metal ... ...

Abstract	Metal ions are crucial for protein function. They participate in enzyme catalysis, play regulatory roles, and help maintain protein structure. Current tools for predicting metal-protein interactions are based on proteins crystallized with their metal ions present (holo forms). However, a majority of resolved structures are free of metal ions (apo forms). Moreover, metal binding is a dynamic process, often involving conformational rearrangement of the binding pocket. Thus, effective predictions need to be based on the structure of the apo state. Here, we report an approach that identifies transition metal-binding sites in apo forms with a resulting selectivity >95%. Applying the approach to apo forms in the Protein Data Bank and structural genomics initiative identifies a large number of previously unknown, putative metal-binding sites, and their amino acid residues, in some cases providing a first clue to the function of the protein.
MeSH term(s)	Apoproteins/chemistry ; Apoproteins/metabolism ; Binding Sites ; Metals/metabolism ; Protein Conformation
Chemical Substances	Apoproteins ; Metals
Language	English
Publishing date	2008-01-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.21587
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Article: The limit of accuracy of protein modeling: influence of crystal packing on protein structure.

Eyal, Eran / Gerzon, Sergey / Potapov, Vladimir / Edelman, Marvin / Sobolev, Vladimir

Journal of molecular biology

2005 Volume 351, Issue 2, Page(s) 431–442

Abstract: 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 ... ...

Abstract	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 the asymmetric unit or whose structures were determined at least twice by X-ray crystallography were paired and their differences analyzed. We demonstrate a clear influence of crystal environment on protein structure, including backbone conformations, hinge-like motions and side-chain conformations. The positions of surface water molecules tend to be variable in different crystal environments while those of ligands are not. Structures determined by independent groups vary more than structures determined by the same authors. The use of different refinement methods is a major source for this effect. Our pair-wise analysis derives a practical limit to the accuracy of protein modeling. For different crystal forms, the limit of accuracy (C(alpha), root-mean-square deviation (RMSD)) is approximately 0.8A for the entire protein, which includes approximately 0.3A due to crystal packing. For organized secondary elements, the upper limit of C(alpha) RMSD is 0.5-0.6A while for loops or protein surface it reaches 1.0A. Twenty percent of exposed side- chains exhibit different chi(1+2) conformations with approximately half of the effect also resulting from crystal packing. A web based tool for analysis and graphic presentation of surface areas of crystal contacts is available (http://ligin.weizmann.ac.il/cryco).
MeSH term(s)	Computational Biology/methods ; Crystallography, X-Ray/methods ; Databases, Protein ; Ligands ; Models, Molecular ; Molecular Conformation ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/chemistry ; Proteomics/methods ; Software ; Solvents ; Water/chemistry
Chemical Substances	Ligands ; Proteins ; Solvents ; Water (059QF0KO0R)
Language	English
Publishing date	2005-08-12
Publishing country	England
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2005.05.066
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Book: Information processing on the basis of processes with competition of modes

Gerzon, S. A

(ITEP ; 1985,177)

1985

Title variant	Pererabotka informacii na osnove processov s konkurenciej mod
Author's details	S. A. Gerzon
Series title	ITEP ; 1985,177
Language	English
Size	8 S
Publishing place	Moscow
Document type	Book
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment.

Sobolev, Vladimir / Eyal, Eran / Gerzon, Sergey / Potapov, Vladimir / Babor, Mariana / Prilusky, Jaime / Edelman, Marvin

Nucleic acids research

2005 Volume 33, Issue Web Server issue, Page(s) W39–43

Abstract: 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 ... ...

Abstract	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 LPC/CSU, analyses of water molecules and nucleic acids have been added, together with improved and expanded visualization options using Chime or Java based Jmol. The SPACE suite includes servers and programs for: structural analysis of point mutations (MutaProt); side chain modeling based on surface complementarity (SCCOMP); building a crystal environment and analysis of crystal contacts (CryCo); construction and analysis of protein contact maps (CMA) and molecular docking software (LIGIN). The SPACE suite is accessed at http://ligin.weizmann.ac.il/space.
MeSH term(s)	Amino Acids/chemistry ; Crystallography, X-Ray ; Databases, Protein ; Internet ; Models, Molecular ; Molecular Structure ; Nucleic Acids/chemistry ; Point Mutation ; Protein Conformation ; Proteins/chemistry ; Proteins/genetics ; Software ; Water/chemistry
Chemical Substances	Amino Acids ; Nucleic Acids ; Proteins ; Water (059QF0KO0R)
Language	English
Publishing date	2005-07-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2205588-5
ISSN	1362-4962 ; 1746-8272 ; 0305-1048 ; 0261-3166
ISSN (online)	1362-4962 ; 1746-8272
ISSN	0305-1048 ; 0261-3166
DOI	10.1093/nar/gki398
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Article: Avtomatizirovannoe rabochee mesto ékonomista.

Gerzon, S S / Gerzon, E I / Norkina, D I / Chermoshentseva, N V / Bochkova, I V

Meditsinskaia tekhnika

1987 , Issue 4, Page(s) 45–47

Title translation	Automated work station for an economist.
MeSH term(s)	Computers ; Economics ; Humans ; Medical Laboratory Science/manpower ; Office Automation ; USSR
Language	Russian
Publishing date	1987-07
Publishing country	Russia (Federation)
Document type	Journal Article
ZDB-ID	390691-7
ISSN	0025-8075 ; 0047-6617
ISSN	0025-8075 ; 0047-6617
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Book: Advokat v sovetskom graždanskom processe

Antimonov, Boris Sergeevič / Gerzon, S. L

posobie dlja advokatov

1954

Institution	Vsesojuznyj Institut juridičeskich nauk Ministerstva justicii SSSR
Author's details	B. S. Antimonov i S. L. Gerzon. Vsesojuznyj Institut juridičeskich nauk Ministerstva justicii SSSR
Language	Russian
Size	258 S
Publisher	Gosjurizdat
Publishing place	Moskva
Document type	Book
Note	In kyrill. Schr. ; Der Advokat im sowjetischen Zivilprozess. Handbuch für Advokaten
Database	Former special subject collection: coastal and deep sea fishing

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Book: Advokat v sovetskom graždanskom processe

Antimonov, Boris Sergeevič / Gerzon, S. L

posobie dlja advokatov

1954

Institution	Vsesojuznyj Institut juridičeskich nauk Ministerstva justicii SSSR
Author's details	B. S. Antimonov i S. L. Gerzon. Vsesojuznyj Institut juridičeskich nauk Ministerstva justicii SSSR
Keywords	Rechtsbeistand ; Russland
Language	Russian
Size	258 S
Publisher	Gosjurizdat
Publishing place	Moskva
Document type	Book
Note	In kyrill. Schr. ; Der Advokat im sowjetischen Zivilprozess. Handbuch für Advokaten
Database	ECONomics Information System

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Article: Direct measurement of the pion valence-quark momentum distribution, the pion light-cone wave function squared.

Aitala, E M / Amato, S / Anjos, J C / Appel, J A / Ashery, D / Banerjee, S / Bediaga, I / Blaylock, G / Bracker, S B / Burchat, P R / Burnstein, R A / Carter, T / Carvalho, H S / Copty, N K / Cremaldi, L M / Darling, C / Denisenko, K / Deval, S / Fernandez, A /

Fox, G F / Gagnon, P / Gerzon, S / Gobel, C / Gounder, K / Halling, A M / Herrera, G / Hurvits, G / James, C / Kasper, P A / Kwan, S / Langs, D C / Leslie, J / Lichtenstadt, J / Lundberg, B / MayTal-Beck, S / Meadows, B / de Mello Neto, J R / Mihalcea, D / Milburn, R H / de Miranda, J M / Napier, A / Nguyen, A / d'Oliveira, A B / O'Shaughnessy, K / Peng, K C / Perera, L P / Purohit, M V / Quinn, B / Radeztsky, S / Rafatian, A / Reay, N W / Reidy, J J / dos Reis, A C / Rubin, H A / Sanders, D A / Santha, A K / Santoro, A F / Schwartz, A J / Sheaff, M / Sidwell, R A / Slaughter, A J / Sokoloff, M D / Solano, J / Stanton, N R / Stefanski, R J / Stenson, K / Summers, D J / Takach, S / Thorne, K / Tripathi, A K / Watanabe, S / Weiss-Babai, R / Wiener, J / Witchey, N / Wolin, E / Yang, S M / Yi, D / Yoshida, S / Zaliznyak, R / Zhang, C

Physical review letters

2001 Volume 86, Issue 21, Page(s) 4768–4772

Abstract: We present the first direct measurements of the pion valence-quark momentum distribution which is related to the square of the pion light-cone wave function. The measurements were carried out using data on diffractive dissociation of 500 GeV/c pi(-) into ...

Abstract	We present the first direct measurements of the pion valence-quark momentum distribution which is related to the square of the pion light-cone wave function. The measurements were carried out using data on diffractive dissociation of 500 GeV/c pi(-) into dijets from a platinum target at Fermilab experiment E791. The results show that the /q&q> light-cone asymptotic wave function describes the data well for Q2 approximately 10 (GeV/c)(2) or more. We also measured the transverse momentum distribution of the diffractive dijets.
Language	English
Publishing date	2001-05-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.86.4768
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Article: Observation of color-transparency in diffractive dissociation of pions.

Physical review letters

2001 Volume 86, Issue 21, Page(s) 4773–4777

Abstract: We have studied the diffractive dissociation into dijets of 500 GeV/c pions scattering coherently from carbon and platinum targets. Extrapolating to asymptotically high energies (where t(min)-->0), we find that when the per-nucleus cross section for this ...

Abstract	We have studied the diffractive dissociation into dijets of 500 GeV/c pions scattering coherently from carbon and platinum targets. Extrapolating to asymptotically high energies (where t(min)-->0), we find that when the per-nucleus cross section for this process is parametrized as sigma = sigma0Aalpha, alpha has values near 1.6, the exact result depending on jet transverse momentum. These values are in agreement with those predicted by theoretical calculations of color-transparency.
Language	English
Publishing date	2001-05-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.86.4773
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Article: Observation of the Cabibbo-Suppressed Decay Ξ_{c}^{+} → pK^{-}π^{+}.

Jun, S Y / Akchurin, N / Andreev, V A / Atamantchouk, A G / Aykac, M / Balatz, M Y / Bondar, N F / Bravar, A / Cooper, P S / Dauwe, L J / Davidenko, G V / Dersch, U / Dolgolenko, A G / Dreossi, D / Dzyubenko, G B / Edelstein, R / Emediato, L / Endler, A M / Engelfried, J /

Eschrich, I / Escobar, C O / Evdokimov, A V / Filimonov, I S / Garcia, F G / Gaspero, M / Gerzon, S / Giller, I / Golovtsov, V L / Goncharenko, Y M / Gottschalk, E / Gouffon, P / Grachov, O A / Gülmez, E / Iori, M / Kamenski, A D / Kangling, H / Kaya, M / Kilmer, J / Kim, V T / Kochenda, L M / Königsmann, K / Konorov, I / Kozhevnikov, A A / Krivshich, A G / Krüger, H / Kubantsev, M A / Kubarovsky, V P / Kulyavtsev, A I / Kuropatkin, N P / Kurshetsov, V F / Kushnirenko, A / Kwan, S / Lach, J / Lamberto, A / Landsberg, L G / Larin, I / Leikin, E M / Luksys, M / Lungov, T / Magarrel, D / Maleev, V P / Mao, D / Masciocchi, S / Mathew, P / Mattson, M / Matveev, V / McCliment, E / McKenna, S L / Moinester, M A / Molchanov, V V / Morelos, A / Mukhin, V A / Nelson, K D / Nemitkin, A V / Neoustroev, P V / Newsom, C / Nilov, A P / Nurushev, S B / Ocherashvili, A / Oleynik, G / Onel, Y / Ozel, E / Ozkorucuklu, S / Patrichev, S / Penzo, A / Petrenko, S I / Pogodin, P / Povh, B / Procario, M / Prutskoi, V A / Ramberg, E / Rappazzo, G F / Razmyslovich, B V / Rud, V I / Russ, J / Schiavon, P / Semyatchkin, V K / Simon, J / Sitnikov, A I / Skow, D / Smith, V J / Srivastava, M / Steiner, V / Stepanov, V / Stutte, L / Svoiski, M / Terentyev, N K / Thomas, G P / Uvarov, L N / Vasiliev, A N / Vavilov, D V / Verebryusov, V S / Victorov, V A / Vishnyakov, V E / Vorobyov, A A / Vorwalter, K / Wenheng, Z / You, J / Yunshan, L / Zhenlin, M / Zhigang, L / Zukanovich Funchal, R

Physical review letters

2000 Volume 84, Issue 9, Page(s) 1857–1861

Abstract: We report the first observation of the Cabibbo-suppressed charm baryon decay Ξ_{c}^{+}→pK^{-}π^{+}. We observe 150±22±5 events for the signal. The data were accumulated using the SELEX spectrometer during the 1996-1997 fixed target run at Fermilab, ... ...

Abstract	We report the first observation of the Cabibbo-suppressed charm baryon decay Ξ_{c}^{+}→pK^{-}π^{+}. We observe 150±22±5 events for the signal. The data were accumulated using the SELEX spectrometer during the 1996-1997 fixed target run at Fermilab, chiefly from a 600 GeV/c Σ^{-} beam. The branching fractions of the decay relative to the Cabibbo-favored Ξ_{c}^{+}→Σ^{+}K^{-}π^{+} and Ξ_{c}^{+}→Ξ^{-}π^{+}π^{+} are measured to be B(Ξ_{c}^{+}→pK^{-}π^{+})/B(Ξ_{c}^{+}→Σ^{+}K^{-}π^{+})=0.22±0.06±0.03 and B(Ξ_{c}^{+}→pK^{-}π^{+})/B(Ξ_{c}^{+}→Ξ^{-}π^{+}π^{+})=0.20±0.04±0.02, respectively.
Language	English
Publishing date	2000-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.84.1857
Database	MEDical Literature Analysis and Retrieval System OnLINE

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