@article {49,
	title = {Activities of Topoisomerase I in Its Complex with SRSF1.},
	journal = {Biochemistry},
	year = {2012},
	month = {02/2012},
	abstract = {Human DNA topoisomerase I (topo I) catalyzes DNA relaxation and phosphorylates SRSF1. Whereas the structure of topo I complexed with DNA has been resolved, the structure of topo I in the complex with SRSF1 and structural determinants of topo I activities in this complex are not known. The main obstacle to resolving the structure is a contribution of unfolded domains of topo I and SRSF1 in formation of the complex. To overcome this difficulty, we employed a three-step strategy: identifying the interaction regions, modeling the complex, and validating the model with biochemical methods. The binding sites in both topo I and SRSF1 are localized in the structured regions as well as in the unfolded domains. One observes cooperation between the binding sites in topo I but not in SRSF1. Our results indicate two features of the unfolded RS domain of SRSF1 containing phosphorylated residues that are critical for the kinase activity of topo I: its spatial arrangement relative to topo I and the organization of its sequence. The efficiency of phosphorylation of SRSF1 depends on the length and flexibility of the spacer between the two RRM domains that uniquely determine an arrangement of the RS domain relative to topo I. The spacer also influences inhibition of DNA nicking, a prerequisite for DNA relaxation. To be phosphorylated, the RS domain has to include a short sequence recognized by topo I. A lack of this sequence in the mutants of SRSF1 or its spatial inaccessibility in SRSF9 makes them inadequate as topo I/kinase substrates.},
	issn = {1520-4995},
	doi = {10.1021/bi300043t},
	author = {Ishikawa, Takao and Krzy{\'s}ko, Krystiana A and Kowalska-Loth, Barbara and Skrajna, Aleksandra M and Czubaty, Alicja and Girstun, Agnieszka and Cieplak, Maja K and Lesyng, Bogdan and Staron, Krzysztof}
}
@article {jozwik2011extraction,
	title = {Extraction of biomedical traits for patients with Amyotrophic Lateral Sclerosis using parallel and hierarchical classifiers},
	journal = {International Journal of Biometrics},
	volume = {3},
	number = {1},
	year = {2011},
	pages = {85{\textendash}94},
	publisher = {Inderscience},
	abstract = {This paper concerns the analysis and interpretation of results obtained from biomedical experiments. The biomedical approach allows differentiating patients by testing their EPO concentration in serum and cerebrospinal fluids. The diagnostic tests can be applied in patient monitoring, or future therapeutic research. The paper presents the possibility of recognition of the clinical status of patients with Amyotrophic Lateral Sclerosis (ALS) by the use of parallel and hierarchical classifiers. The proposed method can be used in biometric identification of ALS patients. The results demonstrate that the pattern recognition methods may be helpful in evaluation of the clinical progress of ALS.},
	author = {J{\'o}{\'z}wik, Adam and Soko{\l}owska, Beata and Niebroj-Dobosz, Irena and Janik, P}
}
@article {5,
	title = {Interaction model based on local protein substructures generalizes to the entire structural enzyme-ligand space.},
	journal = {Journal of chemical information and modeling},
	volume = {48},
	year = {2008},
	month = {2008 Nov},
	pages = {2278-88},
	abstract = {Chemogenomics is a new strategy in in silico drug discovery, where the ultimate goal is to understand molecular recognition for all molecules interacting with all proteins in the proteome. To study such cross interactions, methods that can generalize over proteins that vary greatly in sequence, structure, and function are needed. We present a general quantitative approach to protein-ligand binding affinity prediction that spans the entire structural enzyme-ligand space. The model was trained on a data set composed of all available enzymes cocrystallized with druglike ligands, taken from four publicly available interaction databases, for which a crystal structure is available. Each enzyme was characterized by a set of local descriptors of protein structure that describe the binding site of the cocrystallized ligand. The ligands in the training set were described by traditional QSAR descriptors. To evaluate the model, a comprehensive test set consisting of enzyme structures and ligands was manually curated. The test set contained enzyme-ligand complexes for which no crystal structures were available, and thus the binding modes were unknown. The test set enzymes were therefore characterized by matching their entire structures to the local descriptor library constructed from the training set. Both the training and the test set contained enzyme-ligand complexes from all major enzyme classes, and the enzymes spanned a large range of sequences and folds. The experimental binding affinities (p K i) ranged from 0.5 to 11.9 (0.7-11.0 in the test set). The induced model predicted the binding affinities of the external test set enzyme-ligand complexes with an r (2) of 0.53 and an RMSEP of 1.5. This demonstrates that the use of local descriptors makes it possible to create rough predictive models that can generalize over a wide range of protein targets.},
	keywords = {Animals, Artificial Intelligence, Cluster Analysis, Computer Simulation, Databases, Protein, Drug Discovery, Enzymes, Informatics, Kinetics, Ligands, Models, Molecular, Molecular Structure, Oxidoreductases Acting on CH-CH Group Donors, Oxidoreductases Acting on CH-NH Group Donors, Plasmodium falciparum, Protein Conformation, Zea mays},
	issn = {1549-9596},
	doi = {10.1021/ci800200e},
	author = {Str{\"o}mbergsson, Helena and Daniluk, Pawe{\l} and Kryshtafovych, Andriy and Fidelis, Krzysztof and Wikberg, Jarl E S and Kleywegt, Gerard J and Hvidsten, Torgeir R}
}
@article {52,
	title = {Two novel presenilin 1 gene mutations connected with frontotemporal dementia-like clinical phenotype: genetic and bioinformatic assessment.},
	journal = {Experimental neurology},
	volume = {200},
	year = {2006},
	month = {2006 Jul},
	pages = {82-8},
	abstract = {Mutations in the amyloid precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2) genes are associated with early-onset familial Alzheimer{\textquoteright}s disease (EOAD). There are several reports describing mutations in PSEN1 in cases with frontotemporal dementia (FTD). We identified two novel mutations in the PSEN1 gene: L226F and L424H. The first mutation was detected in a patient with a clinical diagnosis of FTD and a post-mortem diagnosis of AD. The second mutation is connected with a clinical phenotype of variant AD with strong FTD signs. In silico modeling revealed that the mutations, as well as mutations used for comparison (F177L and L424R), change the local structure, stability and/or properties of the transmembrane regions of the presenilin 1 protein (PS1). In contrast, a silent non-synonymous substitution F175S is eclipsed by external residues and has no influence on PS1 interfacial surface. We suggest that in silico analysis of PS1 substitutions can be used to characterize novel PSEN1 mutations, to discriminate between silent polymorphisms and a potential disease-causing mutation. We also propose that PSEN1 mutations should be considered in FTD patients with no MAPT mutations.},
	keywords = {Adult, Computational Biology, Dementia, Diagnosis, Differential, Female, Genetic Testing, Humans, Male, Membrane Proteins, Models, Molecular, Mutation, Phenotype, Presenilin-1},
	issn = {0014-4886},
	doi = {10.1016/j.expneurol.2006.01.022},
	author = {Zekanowski, Cezary and Golan, Maciej P and Krzy{\'s}ko, Krystiana A and Lipczy{\'n}ska-{\L}ojkowska, Wanda and Filipek, S{\l}awomir and Kowalska, Anna and Rossa, Grzegorz and Pep{\l}o{\'n}ska, Beata and Styczy{\'n}ska, Maria and Maruszak, Aleksandra and Religa, Dorota and Wender, Mieczys{\l}aw and Kulczycki, Jerzy and Barcikowska, Maria and Ku{\'z}nicki, Jacek}
}
@article {44,
	title = {CASP6 data processing and automatic evaluation at the protein structure prediction center.},
	journal = {Proteins},
	volume = {61 Suppl 7},
	year = {2005},
	month = {2005},
	pages = {19-23},
	abstract = {We present a short overview of the system governing data processing and automatic evaluation of predictions in CASP6, implemented at the Livermore Protein Structure Prediction Center. The system incorporates interrelated facilities for registering participants, collecting prediction targets from crystallographers and NMR spectroscopists and making them available to the CASP6 participants, accepting predictions and providing their preliminary evaluation, and finally, storing and visualizing results. We have automatically evaluated predictions submitted to CASP6 using criteria and methods developed over the successive CASP experiments. Also, we have tested a new evaluation technique based on non-rigid-body type superpositions. Approximately the same number of predictions has been submitted to CASP6 as to all previous CASPs combined, making navigation through and understanding of the data particularly challenging. To facilitate this, we have substantially modernized all data handling procedures, including implementation of a dedicated relational database. An overview of our redesigned website is also presented (http://predictioncenter.org/casp6/).},
	keywords = {Algorithms, Automation, Computational Biology, Crystallography, X-Ray, Internet, Magnetic Resonance Spectroscopy, Models, Molecular, Protein Conformation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Proteins, Proteomics, Software},
	issn = {1097-0134},
	doi = {10.1002/prot.20718},
	author = {Kryshtafovych, Andriy and Milostan, Maciej and Szajkowski, Lukasz and Daniluk, Pawe{\l} and Fidelis, Krzysztof}
}
@article {53,
	title = {A concept for G protein activation by G protein-coupled receptor dimers: the transducin/rhodopsin interface.},
	journal = {Photochemical \& photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology},
	volume = {3},
	year = {2004},
	month = {2004 Jun},
	pages = {628-38},
	abstract = {G protein-coupled receptors (GPCRs) are ubiquitous and essential in modulating virtually all physiological processes. These receptors share a similar structural design consisting of the seven-transmembrane alpha-helical segments. The active conformations of the receptors are stabilized by an agonist and couple to structurally highly conserved heterotrimeric G proteins. One of the most important unanswered questions is how GPCRs couple to their cognate G proteins. Phototransduction represents an excellent model system for understanding G protein signaling, owing to the high expression of rhodopsin in rod photoreceptors and the multidisciplinary experimental approaches used to study this GPCR. Here, we describe how a G protein (transducin) docks on to an oligomeric GPCR (rhodopsin), revealing structural details of this critical interface in the signal transduction process. This conceptual model takes into account recent structural information on the receptor and G protein, as well as oligomeric states of GPCRs.},
	keywords = {Animals, Dimerization, Models, Molecular, Protein Conformation, Protein Structure, Secondary, Receptors, G-Protein-Coupled, Rhodopsin},
	issn = {1474-905X},
	doi = {10.1039/b315661c},
	author = {Filipek, S{\l}awomir and Krzy{\'s}ko, Krystiana A and Fotiadis, Dimitrios and Liang, Yan and Saperstein, David A and Engel, Andreas and Palczewski, Krzysztof}
}
