Faculty of Biological Sciences

Dr Sergei Krivov

MS, Novosibirsk, Russia PhD 1999, Novosibirsk, Russia
RCUK Academic Research Fellow
School of Molecular and Cellular Biology

Background: Life manifests itself through complex dynamics across many scales, from “wiggling and jiggling of atoms” (protein folding) to transcription dynamics in gene regulatory networks, disease dynamics and population dynamics. Advances in experimental techniques resulted in availability of multidimensional, time-resolved data about dynamical processes. On the other hand, advances in computer hardware and simulation algorithms made it possible to obtain detailed dynamical picture of real-life biological processes on a computer. Computational experiments became a vital component of researches arsenal, as was highlighted by the recent Nobel prize awarded to three computational chemists. The large size of datasets generated by computer simulations or experiments makes the development of automated analysis tools very important, practically and conceptually. In our lab we focus on the development of an original state of the art approach which focuses specifically on accurate description of the dynamics and its application to the analysis of in-silico and in-vitro data.

Contact:  Garstang 10.132, +44(0) 113 34 33141, email address for  

You can read more about Dr Krivov's interests here:
http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=SK

Research Interests

Quantitative analysis of complex biological dynamics.

Faculty Research and Innovation



Studentship information

Undergraduate project topics:

  • Free energy landscape analysis of realistic protein folding simulations.

See also:

Modules managed

BIOL5172M - Practical Bioinformatics

Modules taught

BIOC1303 - Introductory Biochemistry: Problem Solving and Data Handling
BIOC2303 - Intermediate Biochemistry: Skills
BIOL2301 - Intermediate Skills for Biological Sciences
BIOL2301/03/05/MICR2320/BIOL3400 - BIOL/BIOC/MICR advanced skills/Skills in the Cell Biology of Human Disease
BIOL5172M - Practical Bioinformatics
MICR3370 - Microbiology with Virology Research Project

Committees

Member of Masters Taught Student Education Committee

Group Leader Dr Sergei Krivov  (RCUK Academic Research Fellow)

Quantitative analysis of complex biological dynamics. 

Krivov SV The free energy landscape analysis of protein (FIP35) folding dynamics. J Phys Chem B 115 12315-12324, 2011
DOI:10.1021/jp208585r
View abstract

Krivov SV Numerical construction of the p(fold) (committor) reaction coordinate for a Markov process. J Phys Chem B 115 11382-11388, 2011
DOI:10.1021/jp205231b
View abstract

Krivov SV, Karplus M Diffusive reaction dynamics on invariant free energy profiles P NATL ACAD SCI USA 105 13841-13846, 2008
DOI:10.1073/pnas.0800228105

Krivov SV, Muff S, Caflisch A, Karplus M One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process J PHYS CHEM B 112 8701-8714, 2008
DOI:10.1021/jp711864r

Krivov SV, Karplus M One-dimensional free-energy profiles of complex systems: Progress variables that preserve the barriers J PHYS CHEM B 110 12689-12698, 2006
DOI:10.1021/jp060039b

Krivov SV, Karplus M Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci U S A 101 14766-14770, 2004
DOI:10.1073/pnas.0406234101
View abstract

Krivov SV, Karplus M Free energy disconnectivity graphs: Application to peptide models J CHEM PHYS 117 10894-10903, 2002
DOI:10.1063/1.1517606

Banushkina PV, Krivov SV Optimal reaction coordinates Wiley Interdisciplinary Reviews: Computational Molecular Science 6 748-763, 2016
DOI:10.1002/wcms.1276
View abstract

Banushkina PV, Krivov SV Nonparametric variational optimization of reaction coordinates Journal of Chemical Physics 143 -, 2015
DOI:10.1063/1.4935180
View abstract

Banushkina PV, Krivov SV Fep1d: A Script for the Analysis of Reaction Coordinates Journal of Computational Chemistry 36 878-882, 2015
DOI:10.1002/jcc.23868
View abstract

Banushkina PV, Krivov SV High-resolution free energy landscape analysis of protein folding Biochemical Society Transactions 43 157-161, 2015
DOI:10.1042/BST20140260

Krivov SV, Fenton H, Goldsmith PJ, Prasad RK, Fisher J, Paci E Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant. PLoS Computational Biology 10 -, 2014
DOI:10.1371/journal.pcbi.1003685
View abstract

Tian P, Jónsson SA, Ferkinghoff-Borg J, Krivov SV, Lindorff-Larsen K, Irbäck A, Boomsma W Robust estimation of diffusion-optimized ensembles for enhanced sampling Journal of Chemical Theory and Computation 10 543-553, 2014
DOI:10.1021/ct400844x
View abstract

Krivov SV Method to describe stochastic dynamics using an optimal coordinate Physical Review E: Statistical, Nonlinear, and Soft Matter Physics 88 -, 2013
DOI:10.1103/PhysRevE.88.062131
View abstract

Banushkina PV, Krivov SV High-Resolution Free-Energy Landscape Analysis ofα-Helical Protein Folding: HP35 and Its Double Mutant. Journal of Chemical Theory and Computation 9 5257-5266, 2013
DOI:10.1021/ct400651z
View abstract

Radou G, Enciso M, Krivov SV, Paci E Modulation of a protein free-energy landscape by circular permutation Journal of Physical Chemistry B 117 13743-13747, 2013
DOI:10.1021/jp406818t
View abstract

Krivov SV On reaction coordinate optimality Journal of Chemical Theory and Computation 9 135-146, 2013
DOI:10.1021/ct3008292
View abstract

Krivov SV Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape. Phys Rev E Stat Nonlin Soft Matter Phys 84 011135-, 2011
DOI:10.1103/PhysRevE.84.011135
View abstract

Krivov SV Is Protein Folding Sub-Diffusive? PLOS COMPUT BIOL 6 -, 2010
DOI:10.1371/journal.pcbi.1000921

Cecchini M, Krivov SV, Spichty M, Karplus M Erratum: Calculation of free-energy differences by confinement simulations. Application to peptide conformers (Journal of Physical Chemistry B (2009) 113B) Journal of Physical Chemistry B 114 6763-, 2010
DOI:10.1021/jp102878c

Cecchini M, Krivov SV, Spichty M, Karplus M Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers J PHYS CHEM B 113 9728-9740, 2009
DOI:10.1021/jp9020646

Allen LR, Krivov SV, Paci E Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations PLOS COMPUT BIOL 5 -, 2009
DOI:10.1371/journal.pcbi.1000428

Auer S, Miller MA, Krivov SV, Dobson CM, Karplus M, Vendruscolo M Importance of metastable states in the free energy landscapes of polypeptide chains. Phys Rev Lett 99 178104-, 2007
DOI:10.1103/PhysRevLett.99.178104
View abstract

Palyanov AY, Krivov SV, Karplus M, Chekmarev SF A lattice protein with an amyloidogenic latent state: Stability and folding kinetics J PHYS CHEM B 111 2675-2687, 2007
DOI:10.1021/jp067027a

Chekmarev SF, Krivov SV, Karplus M Folding of ubiquitin: A simple model describes the strange kinetics J PHYS CHEM B 110 8865-8869, 2006
DOI:10.1021/jp056799o

Chekmarev SF, Krivov SV, Karplus M Folding time distributions as an approach to protein folding kinetics J PHYS CHEM B 109 5312-5330, 2005
DOI:10.1021/jp047012h

Krivov SV Hierarchical global optimization of quasiseparable systems: application to Lennard-Jones clusters. Phys Rev E Stat Nonlin Soft Matter Phys 66 025701-, 2002
DOI:10.1103/PhysRevE.66.025701
View abstract

Krivov SV, Chekmarev SF, Karplus M Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide. Phys Rev Lett 88 038101-, 2002
DOI:10.1103/PhysRevLett.88.038101
View abstract

Krivov SV, Chekmarev SF, Karplus M Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide Physical review letters 88 038101-, 2002
View abstract

Krivov SV, Chekmarev SF, Karplus M Investigation of the potential surface of tetraalanine-peptide by sequentially locking the molecular dynamic trajectory of the system in attraction basins J STRUCT CHEM+ 42 877-881, 2001

Chekmarev SF, Krivov SV Confinement of the molecular dynamics trajectory to a specified catchment area on the potential surface CHEM PHYS LETT 287 719-724, 1998

Chekmarev SF, Krivov SV Total and fractional densities of states from caloric relations PHYS REV E 57 2445-2448, 1998