Publications

Journals

Catarina Milheiriço, Ana Portelinha, Ludwig Krippahl, Hermínia de Lencastre and Duarte C Oliveira (2011). Evidence for a purifying selection acting on the β-lactamase locus in epidemic clones of methicillin-resistant Staphylococcus aureus. BMC Microbiology 2011, 11:76. (open access)

Pedro Barahona, Ludwig Krippahl (2008). Constraint Programming in Structural Bioinformatics. Constraints 13(1-2): 3-20

Monaco S, Gioia M, Rodriguez J, Fasciglione GF, Di Pierro D, Lupidi G, Krippahl L, Marini S, Coletta M., (2007), Modulation of the proteolytic activity of matrix metalloproteinase-2 (gelatinase A) on fibrinogen. Biochem J. 2007 Mar 15;402(3):503-13.

Krippahl L, Palma PN, Moura I., Moura JG. Modelling the Electron-Transfer Complex Between Aldehyde Oxidoreductase and Flavodoxin (2006). Eur. J. of Inor. Chem., in press

Palma PN, Lagoutte B, Krippahl L, Moura JJ, Guerlesquin F. Synechocystis ferredoxin / ferredoxin - NADP(+)-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking. (2005) FEBS Lett. 2005 Aug 29;579(21):4585-90.

Impagliazzo A, Krippahl L and Ubbink M. Pseudoazurin : Nitrite Reductase Interactions (2005) ChemBioChem 6, 1648-1653 Download .pdf

M.M. Correia dos Santos, P.M.Paes de Sousa, M.L.Simões Gonçalves, L. Krippahl, J.J.G.Moura, É.Lojou, P.Bianco. Electrochemical studies on small electron transfer proteins using membrane electrodes (2003). J. Electroanal. Chem. 541 pp 153-162 (abstract).

Krippahl, L., Moura, J.J., Palma, P.N., Modeling Protein Complexes with BiGGER (2003). Proteins. 2003 Jul 1;52(1):19-23. Download .pdf

Krippahl, L., Barahona, P., PSICO: Solving Protein Structures with Constraint Programming and Optimisation, Constraints 2002, 7, 317-331. Download .pdf

Palma, P.N., Krippahl, L.,Wampler, J.W., Moura, J.G., A New (Soft)Docking Algorithm for Predicting Protein Interactions. Protein:Struc. Func. Gen. 2000 Jun 1;39(4):372-84.

Morelli, X., Dolla, A. Czjezek, M., Palma, P., Blasco, F., Krippahl, L., Moura, J.J.G. & Guerlesquin, F., Heteronuclear NMR and Soft Docking: An Experimental Approach for a Structural Model of the Cytochrome c553/Ferredoxin Complex, Biochemistry. 2000 Mar 14;39(10):2530-7. Download .pdf

Pettigrew, G.W., Prazeres, S., Costa, C., Palma, P.N., Krippahl, L., Moura, I. and Moura, J.J.G.The Structure of an Electron Transfer Complex Containing a Cytochrome c and a Peroxidase, J. Biol. Chem. 1999.Apr 16;274(16):11383-9.

Pettigrew, G.W., Gilmour, R., Goodhew, C.F., Hunter, D.J.B., Devreese, B., Beeumen, J.Van, Costa, C., Prazeres, S., Krippahl, L., Palma, P.N., Moura, I. and Moura, J.J.G. The surface-charge asymmetry and dimerisation of cytochrome c550 from Paracoccus denitrificans - implications for the interaction with cytochrome c peroxidase, Eur. J. Biochem 258, 559-566, 1998.

Book chapters

Pedro Barahona, Ludwig Krippahl and Olivier Perriquet. Bioinformatics: A Challenge to Constraint Programming, in: Michela Milano and Pascal Van Hentenryck (eds), Hybrid Optimization, Springer Optimization and its Applications, Springer, ISBN 978-1-4419-1643-3, Pag. 463-85, 2011.

Published Conference Proceedings

Olivier Perriquet, Marco Correia, Pedro Barahona, and Ludwig Krippahl. A Low resolution Model for Protein Structure Prediction from NMR Data. (EPIA 2007), Guimarães, Portugal (3rd - 7th December 2007), 565-576

José Santos, Pedro Barahona, and Ludwig Krippahl. Mining Protein Structure Data. (EPIA 2007), Guimarães, Portugal (3rd - 7th December 2007), 527-540

Pedro Barahona, Ludwig Krippahl. A Constraint Programming Approach to Bioinformatics Structural Problems. PADL 2007: 33-49

Ludwig Krippahl, Multiple partners in weak interactions, 2nd European Conference on Chemistry for Life Sciences Wroclaw (Poland), 4-8 September 2007, Medimond International Proceedings (2007).

Krippahl, L. Integrating Web Resources to Model Protein Structure and Function. RW-SISS-'2006 (Procs.), Pedro Barahona (Ed.), Lecture Notes in Computer Science, vol. 4126, Springer, pp. 184-196, September 2006.

Krippahl, L, Barahona P. Applying Constraint Programming to Rigid Body Protein Docking (2005), Principles and Practice of Constraint Programming, CP'2005 (Procs.), Peter van Beek (Ed.), Lecture Notes in Computer Science, vol. 3709, Springer, pp. 373-387, October, 2005. Download .pdf

Krippahl, L, Barahona P, Propagating N-ary Rigid-Body Constraints, (2003). Principles and Practice of Constraint Programming, CP'2003 (Procs.), Francesca Rossi (Ed.), Lecture Notes in Computer Science, vol. 2833, Springer, pp. 452-465, October, 2003. Download .pdf

Other

Krippahl, L. and Barahona P., Elucidating transient protein interactions with multiple dockings. WCB 07: Workshop on Constraint-Based Methods for Bioinformatics, Porto, September 13 2007

Krippahl, L and Barahona, P. Chemera: Constraints in Protein Structural Problems, in: Alessandro Dal Palu, Agostino Dovier and Sebastian Will (eds), Proceedings of WCB06, Workshop on Constraint Based Methods for Bioinformatics, Nantes, France, Pag. 30-45, September 2006.

Krippahl, L, Barahona, P, Moura, JJG. Constrained Protein Docking with Chemera 3.0, 2005, BKDB2005 - Bioinformatics: Knowledge Discovery in Biology, Lisboa, Portugal, June 17, 2005

Krippahl, L. 2003. Integrating Protein Structural Information. Ph.D. Dissertation. Download.pdf

Krippahl, L. 2002, The Null Hypothesis. The Skeptic. Download.pdf

Krippahl L., Trosset M., Barahona P. 2001. Combining Constraint Programming and Multidimensional Scaling to solve Distance Geometry Problems. Proceedings of the Third Int. Workshop on Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems, Wye College (Imperial College), 2001, Ashford, Kent UK. Download.pdf

Krippahl,L., Barahona,P. 2000. PSICO: Combining Constraint Programming and Optimisation to Solve Macromolecular Structures, ERCIM 2000 Padova, Italy

Krippahl, L. 1999. Determinação da Estrutura de Proteínas através de Programação por Restrições. Ms.C. Dissertation. Download .pdf (in Portuguese)

Krippahl, L, Barahona, P., 1999. Mixed Constructive-Reparative Solving for Protein Structure Determination, 2nd International Workshop, EKDB-99, Évora, Portugal

Krippahl L., Palma N., Wampler J. and Moura JJG, 1997. Automating Macromolecular Docking on Personal Computers, Second European Conference on Computational Chemistry. Lisboa, Portugal.

Krippahl L., Palma N., Wampler J. and Moura JJG, 1997. Computer Assisted Modeling of Macromolecular Complexes (Maio 1997), Chemistry of Metals in Biological Systems, Tomar, Portugal.

Krippahl L., Palma N., Wampler J. and Moura JJG, 1997. A New Fast and Effective Algorithm for Modelling Macromolecular Interactions, Síntese, Reactividade e Estrutura em Química Inorgânica, Fátima, Portugal.

Krippahl L., Palma N. and Moura JJG, 1996. A New Binary Algorithm for Molecular Docking, Perspectives in Protein Engineering, Monpellier, France.