SAPro

Journal Publications

Journal of Computational Science Vol 1(1): Uphill Unfolding of Native Protein Conformations in Cubic Lattices (A. Albrecht, L. Kapsokalivas, K. Steinhöfel)
APBC 2010: A hybrid approach to protein folding problem integrating constraint programming with local search (A. Z. M. Dayem Ullah, K. Steinhöfel) BMC Bioinformatics Vol. 11 Suppl. 1, 2010: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)
Computational Biology and Chemistry Vol. 33 (4), 2009: Population-based local search for protein folding simulation in the MJ energy model and cubic lattices (L. Kapsokalivas, Xiangchao Gan, A. Albrecht, K. Steinhöfel)
BMC Bioinformatics 2008, 9:209: Discovering biclusters in gene expression data based on high-dimensional linear geometries (Xiangchao Gan, Alan Wee-Chung Liew, Hong Yan)
Computational Biology and Chemistry Vol. 32 (4), 2008: Stochastic Protein Folding Simulation in the Three-dimensional HP-Model (A. Albrecht, A. Skaliotis, K. Steinhöfel)
Computer Physics Communications Vol. 176, Issue 7, 2007: Relating Time Complexity of Protein Folding Simulation to Approximations of Folding Time (K. Steinhöfel, A. Skaliotis, A. Albrecht.)

Conference Publications

EvoBIO 2010: A Replica Exchange Monte Carlo Algorithm for the Optimization of Secondary Structure Packing in Proteins (L. Kapsokalivas, K. Steinhöfel)
LNCS 6023 pp 146-157 Springer 2010
LION 2010: Stochastic Local Search for the Optimization of Secondary Structure Packing in Proteins (L. Kapsokalivas)
LNCS 6073 pp 224-227 Springer 2010
CSBW in IEEE BIBM 2009: Upper Bounds for Foldings in the FCC-HP Protein Model (A. Z. M. Dayem Ullah, K. Steinhöfel)
Proc. IEEE International Conference on Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009, pp. 101 - 106
ISICA 2009: Protein Folding Simulation by Two-stage optimization (A. Z. M. Dayem Ullah, M. Mann, L. Kapsokalivas, K. Steinhöfel)
CCIS Vol. 51 pp. 138-145 Springer 2009
WCB 2009: Constraint-based local move definitions for lattice protein models including side chains (M. Mann, M. A. Hamra, K. Steinhöfel, R. Backofen)
Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB '09)
WABI 2008: A Local Move Set for Protein Folding in Triangular Lattice Models (H.J. Boeckenhauer, A. Z. M. Dayem Ullah, L. Kapsokalivas, K. Steinhöfel)
LNCS Vol. 5251 pp. 369-381 Springer 2008
IEEE WCCI-CEC 2008: Combinatorial Landscape Analysis for k-SAT Instances (A. Albrecht, P.C.R. Lane, K. Steinhöfel)
Proc. IEEE Congress on Evolutionary Computation, pp. 2498-2504, IEEE Press, 2008
10th International Symposium on Artificial Intelligence and Mathematics, ISAIM 2008: Estimating the number of local maxima for k-SAT Instances (A. Albrecht, P.C.R. Lane, K. Steinhöfel)
BIRD 2008: A Symmetry-free Subspace for Ab initio Protein Folding Simulations (Xiangchao Gan, L. Kapsokalivas, A. Albrecht, K. Steinhöfel)
CCIS Vol. 13 pp. 128-139 Springer 2008
BIRD 2008: Two local Search Methods for Protein Folding Simulation in the HP and MJ Lattice Models (L. Kapsokalivas, Xiangchao Gan, K. Steinhöfel, A. Albrecht.)
CCIS Vol.13 pp. 167-179 Springer 2008
BIRD 2007: Stochastic Protein Folding Simulation in the d-dimensional HP-Model (K. Steinhöfel, A. Skaliotis, A. Albrecht)
LNCS Vol. 4414 pp. 381-394 Springer 2007
WABI 2006: Landscape Analysis for Protein Folding Simulation in the H-P Model (K. Steinhöfel, A. Skaliotis, A. Albrecht)
LNCS Vol. 4175 pp. 252-261 Spinger 2006
9th International Symposium on Artificial Intelligence and Mathematics ISAIM 2006: Run-time Estimates for Protein Folding Simulation in the H-P Model (A. Albrecht, K. Steinhöfel)

Posters

German Conference in Bioinformatics 2009 Uphill Unfolding of Native Protein Conformations (L. Kapsokalivas, A. Albrecht, K. Steinhofel)
King's College London Postgraduate Competition 2009 Three Different Approaches To Protein Folding (Abu Zafer M Dayem Ullah) [PDF] Competition 's Winner
King's College London Postgraduate Competition 2008 Stochastic Algorithms for Protein Folding (Leonidas Kapsokalivas) [PDF]

Talks

LSD & LAW 2010 Stochastic Local Search for the Optimization of Secondary Structure Packing in Proteins (Leonidas Kapsokalivas)[Slides]
Intelligent Systems Laboratory Bristol University Population-based Local Search for Protein Folding (Leonidas Kapsokalivas)[Slides]
Computer Science Dep. Leicester University Population-based Local Search for Protein Folding (Leonidas Kapsokalivas)
Visiting Centre for Cancer Research Queen's University Belfast Population-based Local Search for Protein Folding in Rectangular Lattice Models with the MJ Energy Function (Leonidas Kapsokalivas)
Bioinformatics Seminar at King's Guys Campus: Local Search Algorithms in Bioinformatics (Kathleen Steinhöfel)
BCTCS 2008: A Local Move Set for Protein Folding in Triangular Lattice Models (Kathleen Steinhöfel, H.J. Böckenhauer, A. Dayem Ullah, Leonidas Kapsokalivas)
4th LTCS Seminar 2007: Genetic Algorithm for the Protein Folding Problem using the Pull-Move set (Kathleen Steinhöfel, Leonidas Kapsokalivas, Alexandros Skaliotis) [Slides]
BCTCS 2007: Survey of Genetic Algorithms for the Protein Folding Problem (Kathleen Steinhöfel, Leonidas Kapsokalivas, Alexandros Skaliotis) [Slides]
LSD+LAW 2006: Logarithmic Simulated Annealing for Protein Folding (Kathleen Steinhöfel, Alexandros Skaliotis, Andreas A. Albrecht)
BCTCS 2006: Protein Folding in the 2D HP Model (Kathleen Steinhöfel, Alexandros Skaliotis, Andreas A. Albrecht) [Slides]

SAPro Stochastic Local Search Algorithms for Structural Proteomics

Journal Publications

Conference Publications

Posters

Talks

SAPro

Stochastic Local Search Algorithms for Structural Proteomics