@article {42,
	title = {Protein structure prediction center in CASP8.},
	journal = {Proteins},
	volume = {77 Suppl 9},
	year = {2009},
	month = {2009},
	pages = {5-9},
	abstract = {We present an outline of the Critical Assessment of Protein Structure Prediction (CASP) infrastructure implemented at the University of California, Davis, Protein Structure Prediction Center. The infrastructure supports selection and validation of prediction targets, collection of predictions, standard evaluation of submitted predictions, and presentation of results. The Center also supports information exchange relating to CASP experiments and structure prediction in general. Technical aspects of conducting the CASP8 experiment and relevant statistics are also provided.},
	keywords = {Computational Biology, Databases, Protein, Models, Molecular, Protein Conformation, Proteins, Software},
	issn = {1097-0134},
	doi = {10.1002/prot.22517},
	author = {Kryshtafovych, Andriy and Krysko, Oleh and Daniluk, Pawe{\l} and Dmytriv, Zinoviy and Fidelis, Krzysztof}
}
@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 {43,
	title = {New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.},
	journal = {Proteins},
	volume = {69 Suppl 8},
	year = {2007},
	month = {2007},
	pages = {19-26},
	abstract = {We outline the main tasks performed by the Protein Structure Prediction Center in support of the CASP7 experiment and provide a brief review of the major measures used in the automatic evaluation of predictions. We describe in more detail the software developed to facilitate analysis of modeling success over and beyond the available templates and the adopted Java-based tool enabling visualization of multiple structural superpositions between target and several models/templates. We also give an overview of the CASP infrastructure provided by the Center and discuss the organization of the results web pages available through http://predictioncenter.org.},
	keywords = {Computational Biology, Internet, Models, Molecular, Protein Conformation, Protein Folding, Proteins, Software, Structure-Activity Relationship},
	issn = {1097-0134},
	doi = {10.1002/prot.21653},
	author = {Kryshtafovych, Andriy and Prlic, Andreas and Dmytriv, Zinoviy and Daniluk, Pawe{\l} and Milostan, Maciej and Eyrich, Volker and Hubbard, Tim and Fidelis, Krzysztof}
}
@article {51,
	title = {Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment.},
	journal = {Biochimica et biophysica acta},
	volume = {1758},
	year = {2006},
	month = {2006 Apr},
	pages = {537-44},
	abstract = {Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard-Jones contact interactions is applied to model the protein-membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins.},
	keywords = {Bacterial Proteins, Bacteriorhodopsins, Cell Membrane, Computer Simulation, Halobacterium salinarum, Lipid Bilayers, Models, Molecular, Protein Conformation, Protein Denaturation, Protein Structure, Secondary},
	issn = {0006-3002},
	doi = {10.1016/j.bbamem.2006.03.028},
	author = {Cieplak, Marek and Filipek, S{\l}awomir and Janovjak, Harald and Krzy{\'s}ko, Krystiana A}
}
@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}
}
