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1

The Classification and Origins of Protein Folding Patterns

Chothia, Cyrus, Finkelstein, Alexei V.

Journal:

Annual Review of Biochemistry

Year:

1990

Language:

english

File:

PDF, 999 KB

english, 1990

2

Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold: Influence of chain knotting on the rate of folding

Alexei V Finkelstein, Azat Ya Badretdinov

Journal:

Folding and Design

Year:

1998

Language:

english

File:

PDF, 46 KB

english, 1998

3

Making optimal use of empirical energy functions: Force-field parameterization in crystal space

Elmar Krieger, Tom Darden, Sander B. Nabuurs, Alexei Finkelstein, Gert Vriend

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 238 KB

english, 2004

4

What is the probability of a chance prediction of a protein structure with an rmsd of 6 å?

Boris A Reva, Alexei V Finkelstein, Jeffrey Skolnick

Journal:

Folding and Design

Year:

1998

Language:

english

File:

PDF, 118 KB

english, 1998

5

The price of lost freedom: entropy of bimolecular complex formation

Finkelstein, Alexei V., Janin, Joël

Journal:

Protein Engineering Design and Selection

Year:

1989

Language:

english

File:

PDF, 322 KB

english, 1989

6

Protein Physics || Lecture 3

Finkelstein, Alexei V.

Year:

2016

Language:

english

File:

PDF, 1.20 MB

english, 2016

7

Lattice modeling: Accuracy of energy calculations

Reva, Boris A., Sanner, Michel F., Olson, Arthur J., Finkelstein, Alexei V.

Journal:

Journal of Computational Chemistry

Year:

1996

Language:

english

File:

PDF, 538 KB

english, 1996

8

Adjusting potential energy functions for lattice models of chain molecules

Reva, Boris A., Finkelstein, Alexei V., Sanner, Michel F., Olson, Arthur J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 696 KB

english, 1996

9

Building self-avoiding lattice models of proteins using a self-consistent field optimization

Reva, Boris A., Finkelstein, Alexei V., Rykunov, Dmitrii S., Olson, Arthur J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 593 KB

english, 1996

10

Averaging interaction energies over homologs improves protein fold recognition in gapless threading

Boris A. Reva, Jeffrey Skolnick, Alexei V. Finkelstein

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 67 KB

english, 1999

11

Oleg Borisovich Ptitsyn: July 18, 1929–March 22, 1999

Alexei Finkelstein

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 61 KB

english, 1999

12

Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

Alexei V Finkelstein

Journal:

Chemistry Central Journal

Year:

2007

Language:

english

File:

PDF, 1.16 MB

english, 2007

13

How strong are side chain interactions in the folding intermediate?

Ekaterina N. Samatova, Natalia S. Katina, Vitaly A. Balobanov, Bogdan S. Melnik, Dmitry A. Dolgikh, Valentina E. Bychkova, Alexei V. Finkelstein

Journal:

Protein Science

Year:

2009

Language:

english

File:

PDF, 539 KB

english, 2009

14

Threading with chemostructural restrictions method for predicting fold and functionally significant residues: Application to dipeptidylpeptidase IV (DPP-IV)

Boris Reva, Alexei Finkelstein, Sid Topiol

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 588 KB

english, 2002

15

Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics

Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, Dmitry N. Ivankov, Alexei V. Finkelstein

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 98 KB

english, 2003

16

From analysis of protein structural alignments toward a novel approach to align protein sequences

Shamil R. Sunyaev, Gennady A. Bogopolsky, Natalia V. Oleynikova, Peter K. Vlasov, Alexei V. Finkelstein, Mikhail A. Roytberg

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 756 KB

english, 2004

17

Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?

Sergiy O. Garbuzynskiy, Bogdan S. Melnik, Michail Yu. Lobanov, Alexei V. Finkelstein, Oxana V. Galzitskaya

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 393 KB

english, 2005

18

Why do protein architectures have boltzmann-like statistics?

Alexei V. Finkelstein, Azat Ya. Badretdinov, Alexander M. Gutin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1995

Language:

english

File:

PDF, 852 KB

english, 1995

19

Perfect temperature for protein structure prediction and folding

Alexei V. Finkelstein, Alexander M. Gutin, Azat Ya. Badretdinov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1995

Language:

english

File:

PDF, 1.04 MB

english, 1995

20

A search for the most stable folds of protein chains

Finkelstein, Alexei V., Reva, Boris A.

Journal:

Year:

1991

File:

PDF, 327 KB

1991

21

10.1038/8211

Finkelstein, Alexei

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 71 KB

english, 1999

22

Three-state protein folding: Experimental determination of free-energy profile

Ekaterina N. Baryshnikova, Bogdan S. Melnik, Alexei V. Finkelstein, Gennady V. Semisotnov, Valentina E. Bychkova

Journal:

Protein Science

Year:

2005

Language:

english

File:

PDF, 697 KB

english, 2005

23

Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold

Alexei V Finkelstein, Azat Ya Badretdinov

Journal:

Folding and Design

Year:

1997

Language:

english

File:

PDF, 102 KB

english, 1997

24

Folding rate dependence on the chain length for RNA-like heteropolymers

Oxana V Galzitskaya, Alexei V Finkelstein

Journal:

Folding and Design

Year:

1998

Language:

english

File:

PDF, 163 KB

english, 1998

25

Folding of circular permutants with decreased contact order: general trend balanced by protein stability

Magnus O Lindberg, Jeanette Tångrot, Daniel E Otzen, Dmitry A Dolgikh, Alexei V Finkelstein, Mikael Oliveberg

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 352 KB

english, 2001

26

Recognition of signal sequences

Alexei V. Finkelstein, Peter Bendzko, Tom A. Rapoport

Journal:

Year:

1983

Language:

english

File:

PDF, 432 KB

english, 1983

27

Secondary structure of globular proteins at the early and the final stages in protein folding

Kunihiro Kuwajima, Gennady V Semisotnov, Alexei V Finkelstein, Shintaro Sugai, Oleg B Ptitsyn

Journal:

Year:

1993

Language:

english

File:

PDF, 521 KB

english, 1993

28

Why are the same protein folds used to perform different functions?

Alexei V. Finkelstein, Alexander M. Gutun, Azat Ya. Badretdinov

Journal:

Year:

1993

Language:

english

File:

PDF, 591 KB

english, 1993

29

Outlining Folding Nuclei in Globular Proteins

Sergiy O. Garbuzynskiy, Alexei V. Finkelstein, Oxana V. Galzitskaya

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.72 MB

english, 2004

30

Folding nuclei in proteins

Oxana V Galzitskaya, Dmitry N Ivankov, Alexei V Finkelstein

Journal:

Year:

2001

Language:

english

File:

PDF, 169 KB

english, 2001

31

Protein structure: what is it possible to predict now?

Alexei V Finkelstein

Journal:

Current Opinion in Structural Biology

Year:

1997

Language:

english

File:

PDF, 1.24 MB

english, 1997

32

Folding Intermediate and Folding Nucleus for I→N and U→I→N Transitions in Apomyoglobin: Contributions by Conserved and Nonconserved Residues

Samatova, Ekaterina N., Melnik, Bogdan S., Balobanov, Vitaly A., Katina, Natalya S., Dolgikh, Dmitry A., Semisotnov, Gennady V., Finkelstein, Alexei V., Bychkova, Valentina E.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 595 KB

english, 2010

33

Levinthal’s question answered … again?

Finkelstein, Alexei V., Garbuzynskiy, Sergiy O.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 93 KB

english, 2013

34

Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida

Chris Sander, Gerrit Vriend, Fernando Bazan, Amnon Horovitz, Haruki Nakamura, Luis Ribas, Alexei V. Finkelstein, Andrew Lockhart, Rainer Merkl, L. Jeanne Perry, Stephen C. Emery, Christine Gaboriaud,

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1992

Language:

english

File:

PDF, 589 KB

english, 1992

35

Protein Folding as Flow across a Network of Folding−Unfolding Pathways. 2. The “In-Water” Case

Ivankov, Dmitry N., Finkelstein, Alexei V.

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 1.27 MB

english, 2010

36

Contact order revisited: Influence of protein size on the folding rate

Dmitry N. Ivankov, Sergiy O. Garbuzynskiy, Eric Alm, Kevin W. Plaxco, David Baker, Alexei V. Finkelstein

Journal:

Protein Science

Year:

2003

Language:

english

File:

PDF, 149 KB

english, 2003

37

Protein Physics || Lecture 18

Finkelstein, Alexei V.

Year:

2002

Language:

english

File:

PDF, 679 KB

english, 2002

38

Protein Physics || Lecture 17

Finkelstein, Alexei V.

Year:

2002

Language:

english

File:

PDF, 1.12 MB

english, 2002

39

Folding of chains with random and edited sequences: similarities and differences

Galzitskaya, Oxana V., Finkelstein, Alexei V.

Journal:

Protein Engineering Design and Selection

Year:

1995

Language:

english

File:

PDF, 2.69 MB

english, 1995

40

Restrictions to protein folding determined by the protein size

Finkelstein, Alexei V., Bogatyreva, Natalya S., Garbuzynskiy, Sergiy O.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

41

Implications of the random characteristics of protein sequences for their three-dimensional structure

Finkelstein, Alexei V.

Journal:

Current Opinion in Structural Biology

Year:

1994

Language:

english

File:

PDF, 633 KB

english, 1994

42

A Theoretical Search for Folding/Unfolding Nuclei in Three-Dimensional Protein Structures

Oxana V. Galzitskaya and Alexei V. Finkelstein

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 1.01 MB

english, 1999

43

Myoglobin-CO Substate Structures and Dynamics: Multidimensional Vibrational Echoes and Molecular Dynamics Simulations

Merchant, Kusai A., Noid, W. G., Akiyama, Ryo, Finkelstein, Ilya J., Goun, Alexei, McClain, Brian L., Loring, Roger F., Fayer, M. D.

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 699 KB

english, 2003

44

Theoretical Study of a Landscape of Protein Folding−Unfolding Pathways. Folding Rates at Midtransition †

Ivankov, Dmitry N., Finkelstein, Alexei V.

Journal:

Year:

2001

Language:

english

File:

PDF, 52 KB

english, 2001

45

Cunning Simplicity of a Hierarchical Folding

Finkelstein, Alexei V.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2002

Language:

english

File:

PDF, 218 KB

english, 2002

46

Protein Folding as Flow across a Network of Folding−Unfolding Pathways. 1. The Mid-Transition Case

Ivankov, Dmitry N., Finkelstein, Alexei V.

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 1.37 MB

english, 2010

47

Computer simulation of secondary structure folding of random and ‘‘edited’’ RNA chains

Galzitskaya, Oxana V., Finkelstein, Alexei V.

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 361 KB

english, 1996

48

3D Protein Folds: Homologs Against Errors—a Simple Estimate Based on the Random Energy Model

Finkelstein, Alexei V.

Journal:

Physical Review Letters

Year:

1998

Language:

english

File:

PDF, 107 KB

english, 1998

49

Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach

REVA, BORIS A., RYKUNOV, D.S., FINKELSTEIN, ALEXEI V., SKOLNICK, JEFFREY

Journal:

Journal of Computational Biology

Year:

1998

Language:

english

File:

PDF, 780 KB

english, 1998

50

How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences

BADRETDINOV, AZAT YA, FINKELSTEIN, ALEXEI V.

Journal:

Journal of Computational Biology

Year:

1998

Language:

english

File:

PDF, 939 KB

english, 1998