@article {4,
	title = {Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {25},
	year = {2009},
	month = {2009 May 15},
	pages = {1264-70},
	abstract = {MOTIVATION: Correct prediction of residue-residue contacts in proteins that lack good templates with known structure would take ab initio protein structure prediction a large step forward. The lack of correct contacts, and in particular long-range contacts, is considered the main reason why these methods often fail.

RESULTS: We propose a novel hidden Markov model (HMM)-based method for predicting residue-residue contacts from protein sequences using as training data homologous sequences, predicted secondary structure and a library of local neighborhoods (local descriptors of protein structure). The library consists of recurring structural entities incorporating short-, medium- and long-range interactions and is general enough to reassemble the cores of nearly all proteins in the PDB. The method is tested on an external test set of 606 domains with no significant sequence similarity to the training set as well as 151 domains with SCOP folds not present in the training set. Considering the top 0.2 x L predictions (L = sequence length), our HMMs obtained an accuracy of 22.8\% for long-range interactions in new fold targets, and an average accuracy of 28.6\% for long-, medium- and short-range contacts. This is a significant performance increase over currently available methods when comparing against results published in the literature.

AVAILABILITY: http://predictioncenter.org/Services/FragHMMent/.},
	keywords = {Computational Biology, Databases, Protein, Markov Chains, Models, Molecular, Protein Folding, Protein Structure, Secondary, Proteins},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btp149},
	author = {Bj{\"o}rkholm, Patrik and Daniluk, Pawe{\l} and Kryshtafovych, Andriy and Fidelis, Krzysztof and Andersson, Robin and Hvidsten, Torgeir R}
}
@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}
}
