- The IntAct molecular interaction database in 2010
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 38:D525-31. 2010
..Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
- Network organization of the human autophagy system
Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
Nature 466:68-76. 2010
..These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway...
- The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Denmark
Nucleic Acids Res 39:D561-8. 2011
..Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org...
- Human Protein Reference Database--2009 update
T S Keshava Prasad
Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
Nucleic Acids Res 37:D767-72. 2009
..Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome...
- The genetic landscape of a cell
Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
Science 327:425-31. 2010
..We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification...
- The BioGRID Interaction Database: 2011 update
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
Nucleic Acids Res 39:D698-704. 2011
..The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions...
- The IntAct molecular interaction database in 2012
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 40:D841-6. 2012
..IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact...
- Interactome networks and human disease
Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
Cell 144:986-98. 2011
- MINT, the molecular interaction database: 2012 update
Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
Nucleic Acids Res 40:D857-61. 2012
..bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction...
- MINT, the molecular interaction database: 2009 update
Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome
Nucleic Acids Res 38:D532-9. 2010
..MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium...
- PID: the Pathway Interaction Database
Carl F Schaefer
National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA
Nucleic Acids Res 37:D674-9. 2009
..The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools...
- KEGG for representation and analysis of molecular networks involving diseases and drugs
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 38:D355-60. 2010
..The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets...
- Link communities reveal multiscale complexity in networks
Yong Yeol Ahn
Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
Nature 466:761-4. 2010
..Our results imply that link communities are fundamental building blocks that reveal overlap and hierarchical organization in networks to be two aspects of the same phenomenon...
- Global landscape of HIV-human protein complexes
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
Nature 481:365-70. 2012
..This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection...
- A global protein kinase and phosphatase interaction network in yeast
Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario, M5G 1X5, Canada
Science 328:1043-6. 2010
..An extensive backbone of kinase-kinase interactions cross-connects the proteome and may serve to coordinate diverse cellular responses...
- An empirical framework for binary interactome mapping
Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA
Nat Methods 6:83-90. 2009
- Computing topological parameters of biological networks
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Bioinformatics 24:282-4. 2008
..It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user...
- Detecting overlapping protein complexes in protein-protein interaction networks
Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK
Nat Methods 9:471-2. 2012
..The results also showed a high extent of functional homogeneity...
- Independently evolved virulence effectors converge onto hubs in a plant immune system network
M Shahid Mukhtar
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Science 333:596-601. 2011
..Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies...
- A protein complex network of Drosophila melanogaster
K G Guruharsha
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
Cell 147:690-703. 2011
..The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution...
- STRING 8--a global view on proteins and their functional interactions in 630 organisms
Lars J Jensen
European Molecular Biology Laboratory, Heidelberg, Germany
Nucleic Acids Res 37:D412-6. 2009
..Version 8.0 of STRING covers about 2.5 million proteins from 630 organisms, providing the most comprehensive view on protein-protein interactions currently available. STRING can be reached at http://string-db.org/...
- Walking the interactome for prioritization of candidate disease genes
Institute for Medical Genetics, Charite Universitatsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
Am J Hum Genet 82:949-58. 2008
- Protein interaction data curation: the International Molecular Exchange (IMEx) consortium
European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
Nat Methods 9:345-50. 2012
..We discuss the advantages of such a service to the user, our quality-control measures and our data-distribution practices...
- BioGRID: a general repository for interaction datasets
Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9
Nucleic Acids Res 34:D535-9. 2006
..User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID...
- Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
Alasdair T R Laurie
School of Biochemistry and Microbiology, University of Leeds, UK
Bioinformatics 21:1908-16. 2005
..Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster...
- iRefIndex: a consolidated protein interaction database with provenance
The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
BMC Bioinformatics 9:405. 2008
..We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping...
- Rewiring of genetic networks in response to DNA damage
Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
Science 330:1385-9. 2010
..Differential networks chart a new type of genetic landscape that is invaluable for mapping cellular responses to stimuli...
- The BioGRID Interaction Database: 2008 update
Bobby Joe Breitkreutz
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
Nucleic Acids Res 36:D637-40. 2008
..Source code for the BioGRID and the linked Osprey network visualization system is now freely available without restriction...
- Associating genes and protein complexes with disease via network propagation
School of Computer Science, Tel Aviv University, Tel Aviv, Israel
PLoS Comput Biol 6:e1000641. 2010
..PRINCE's predictions for these diseases highly match the known literature, suggesting several novel causal genes and protein complexes for further investigation...
- An automated method for finding molecular complexes in large protein interaction networks
Gary D Bader
Samuel Lunenfeld Research Institute, MT, Sinai Hospital, Toronto ON Canada M5G 1X5, Dept, of Biochemistry, University of Toronto, Toronto ON Canada M5S 1A8
BMC Bioinformatics 4:2. 2003
..As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery...
- Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
Hon Nian Chua
Graduate School for Integrated Sciences and Engineering, National University of Singapore, Singapore
Bioinformatics 22:1623-30. 2006
..We are interested in finding out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction...
- ATTED-II provides coexpressed gene networks for Arabidopsis
Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
Nucleic Acids Res 37:D987-91. 2009
..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
- COPASI--a COmplex PAthway SImulator
Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA
Bioinformatics 22:3067-74. 2006
..Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods...
- Up-to-date catalogues of yeast protein complexes
Molecular Structure and Function Program, Hospital for Sick Children, Toronto ON, M5G 1X8
Nucleic Acids Res 37:825-31. 2009
..Some of these partially supported and as yet unsupported complexes may be interesting candidates for experimental follow up. Both catalogues are freely available at: http://wodaklab.org/cyc2008/...
- Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data
Zhu Hong You
Intelligent Computing Laboratory, Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui, China
Bioinformatics 26:2744-51. 2010
..Most previous works for assessing and predicting protein interactions either need supporting evidences from multiple information resources or are severely impacted by the sparseness of PPI networks...
- A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing
Gwendolyn M Wilmes
Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143 2200, USA
Mol Cell 32:735-46. 2008
..Finally, we show that Csn12 plays a role in pre-mRNA splicing, which is independent of other signalosome components. Thus, Sem1 is involved in three separate and functionally distinct complexes...
- SMART 6: recent updates and new developments
EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany
Nucleic Acids Res 37:D229-32. 2009
..In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service...
- Relating protein pharmacology by ligand chemistry
Michael J Keiser
Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St, San Francisco California 94143 2550, USA
Nat Biotechnol 25:197-206. 2007
..These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves...
- ZDOCK: an initial-stage protein-docking algorithm
Bioinformatics Program, Boston University, Boston, Massachusetts, USA
Proteins 52:80-7. 2003
..All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/~ rong/dock...
- Event extraction for systems biology by text mining the literature
University of Manchester, Manchester M13 9PL, UK
Trends Biotechnol 28:381-90. 2010
..The approaches described will be of considerable value in associating particular pathways and their components with higher-order physiological properties, including disease states...
- Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Bioinformatics 24:i232-40. 2008
..Therefore, there is a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently...
- DOMINE: a comprehensive collection of known and predicted domain-domain interactions
Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
Nucleic Acids Res 39:D730-5. 2011
..The contents of the DOMINE are available at http://domine.utdallas.edu...
- The power of protein interaction networks for associating genes with diseases
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies and Department of Computer Science, University of Maryland College Park, College Park, MD 20742, USA
Bioinformatics 26:1057-63. 2010
..Despite the recent interest in this problem, however, there is little understanding of the relative benefits and drawbacks underlying the proposed techniques...
- ConsensusPathDB: toward a more complete picture of cell biology
Vertebrate Genomics Department, Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
Nucleic Acids Res 39:D712-7. 2011
- STITCH 2: an interaction network database for small molecules and proteins
Biotechnology Center, TU Dresden, 01062 Dresden, Germany
Nucleic Acids Res 38:D552-6. 2010
..STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/...
- A human functional protein interaction network and its application to cancer data analysis
Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON M5G 0A3, Canada
Genome Biol 11:R53. 2010
..A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system...
- High-quality binary protein interaction map of the yeast interactome network
Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, MA 02115, USA
Science 322:104-10. 2008
..Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy...
- Dynamic protein-protein interaction wiring of the human spliceosome
Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
Mol Cell 45:567-80. 2012
..Our data provide extensive information about the spliceosomal protein interaction network and its dynamics...
- 3did: identification and classification of domain-based interactions of known three-dimensional structure
Institute for Research in Biomedicine, Join IRB BSC Program in Computational Biology, 08028 Barcelona, Spain
Nucleic Acids Res 39:D718-23. 2011
..The 3did web server at http://3did.irbbarcelona.org visualizes these interfaces along with atomic details of individual interactions using Jmol. The complete contents are also available for download...
- Complex discovery from weighted PPI networks
School of Computing, National University of Singapore, Singapore and Institute for Infocomm Research, Singapore
Bioinformatics 25:1891-7. 2009
..However, protein interaction data produced by high-throughput experiments are often associated with high false positive and false negative rates, which makes it difficult to predict complexes accurately...
- NetPath: a public resource of curated signal transduction pathways
Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
Genome Biol 11:R3. 2010
..We anticipate NetPath to become a consolidated resource for human signaling pathways that should enable systems biology approaches...
- Getting connected: analysis and principles of biological networks
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
Genes Dev 21:1010-24. 2007
..Analyzing these networks provides novel insights in understanding basic mechanisms controlling normal cellular processes and disease pathologies...
- Measuring the evolutionary rate of protein-protein interaction
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
Proc Natl Acad Sci U S A 108:8725-30. 2011
..The extremely slow evolution of protein molecular function may account for the remarkable conservation of life at molecular and cellular levels and allow for studying the mechanistic basis of human disease in much simpler organisms...
- HIPPIE: Integrating protein interaction networks with experiment based quality scores
Martin H Schaefer
Max Delbruck Center for Molecular Medicine, Berlin, Germany
PLoS ONE 7:e31826. 2012
..The HIPPIE web tool (available at http://cbdm.mdc-berlin.de/tools/hippie) allows researchers to do network analyses focused on likely true PPI sets by generating subnetworks around proteins of interest at a specified confidence level...
- PINA v2.0: mining interactome modules
Mark J Cowley
Cancer Research Program, Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
Nucleic Acids Res 40:D862-5. 2012
..The interactome data are also available on the web site for further bioinformatics analysis. PINA is freely accessible at http://cbg.garvan.unsw.edu.au/pina/...
- Identification of direct residue contacts in protein-protein interaction by message passing
Center for Theoretical Biological Physics and Department of Physics, University of California at San Diego, La Jolla, CA 92093 0374, USA
Proc Natl Acad Sci U S A 106:67-72. 2009
- Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA
Genome Biol 10:R91. 2009
..Many of these disease-disease associations are supported by epidemiology, but with no previous genetic basis. Such associations can drive novel hypotheses on molecular mechanisms of diseases and therapies...
- An experimentally derived confidence score for binary protein-protein interactions
Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
Nat Methods 6:91-7. 2009
..This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks...
- Evolution of biomolecular networks: lessons from metabolic and protein interactions
European Molecular Biology Laboratory, Heidelberg, Germany
Nat Rev Mol Cell Biol 10:791-803. 2009
..However, many evolutionary constraints can be uncovered only if temporal and spatial aspects are included in the network analysis...
- GeneCards Version 3: the human gene integrator
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
Database (Oxford) 2010:baq020. 2010
..Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database URL: www.genecards.org...
- Modeling interactome: scale-free or geometric?
Department of Computer Science, University of Toronto, Toronto, M5S 3G4, Canada
Bioinformatics 20:3508-15. 2004
..Since incorrect models lead to incorrect predictions, it is vital to have as accurate a model as possible. As a result, new techniques and models for analyzing and modeling real-world networks have recently been introduced...
- Reverse engineering of regulatory networks in human B cells
Institute for Cancer Genetics, 1300 St Nicholas Avenue, Room 912, New York, New York 10032, USA
Nat Genet 37:382-90. 2005
..The newly identified MYC targets include some major hubs. This approach can be generally useful for the analysis of normal and pathologic networks in mammalian cells...
- DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
Nucleic Acids Res 39:D736-43. 2011
..Improvements have been made to the web and graphical interfaces to help biologists gain a comprehensive view of the interaction networks relevant to the genes and systems that they study...
- ClusPro: an automated docking and discrimination method for the prediction of protein complexes
Stephen R Comeau
Bioinformatics Graduate Program and Department, Boston University, 44 Cummington St, Boston, MA 02215, USA
Bioinformatics 20:45-50. 2004
..e. structures with good surface complementarity but far from the native...
- Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
NEC LABS AMERICA, Princeton, NJ 08540, USA
Bioinformatics 26:i645-52. 2010
..Meanwhile, there exists a considerable amount of protein pairs where an association appears between two partners, but not enough experimental evidence to support it as a direct interaction (partially labeled)...
- Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I)
Interactions et Modulateurs de Réponses UPR3243, Centre National de la Recherche Scientifique CNRS and Université de Provence, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
Curr Opin Chem Biol 15:475-81. 2011
..Finally, ligand efficiency analyses permit us to relate potency to size and polarity and to discuss the need to co-develop nanoparticle drug delivery systems...
- HINT: High-quality protein interactomes and their applications in understanding human disease
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
BMC Syst Biol 6:92. 2012
..A repository of well-validated high-quality protein-protein interactions can be used in both large- and small-scale studies to generate and validate a wide range of functional hypotheses...
- IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
Benjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
Nucleic Acids Res 40:D834-40. 2012
..The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly...
- The ConsensusPathDB interaction database: 2013 update
Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63 73, 14195 Berlin, Germany
Nucleic Acids Res 41:D793-800. 2013
..To facilitate the interactive, visual interpretation of interaction and pathway data, we have re-implemented the graph visualization feature of ConsensusPathDB using the Cytoscape.js library...
- Analysis of the human endogenous coregulator complexome
Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
Cell 145:787-99. 2011
..This resource will effectively fill a void in linking correlative genomic studies with an understanding of transcriptional regulatory protein functions within the proteome for formulation and testing of future hypotheses...
- A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
Knowledge Management in Bioinformatics, Computer Science Department, Humboldt Universitat zu Berlin, Berlin, Germany
PLoS Comput Biol 6:e1000837. 2010
..Nevertheless, our study shows that three kernels are clearly superior to the other methods...
- Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality
Max Planck Institute for Informatics, Saarbruecken, Germany
PLoS Comput Biol 4:e1000140. 2008
- Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis
Section of Genetic Medicine and Center for Biomedical Informatics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
PLoS Comput Biol 6:e1000730. 2010
- Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
College of Chemistry, Sichuan University, Chengdu 610064 and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P R China
Nucleic Acids Res 36:3025-30. 2008
..The prediction software and all data sets used in this article are freely available at http://www.scucic.cn/Predict_PPI/index.htm...
- The impact of multifunctional genes on "guilt by association" analysis
Department of Psychiatry, University of British Columbia, Centre for High Throughput Biology, Vancouver, British Columbia, Canada
PLoS ONE 6:e17258. 2011
..We suggest that this source of bias due to multifunctionality is important to control for, with widespread implications for the interpretation of genomics studies...
- Next-generation sequencing to generate interactome datasets
Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
Nat Methods 8:478-80. 2011
..Stitch-seq is applicable to various interaction assays and should help expand interactome network mapping...
- ClusPro: a fully automated algorithm for protein-protein docking
Stephen R Comeau
Bioinformatics Graduate Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
Nucleic Acids Res 32:W96-9. 2004
..The program output is a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email...
- Inferring cellular networks--a review
Max Planck Institute for Molecular Genetics, Ihnestrasse 63 73, 14195 Berlin, Germany
BMC Bioinformatics 8:S5. 2007
..The second part discusses probabilistic and graph-based methods for data from experimental interventions and perturbations...
- VirusMINT: a viral protein interaction database
Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
Nucleic Acids Res 37:D669-73. 2009
- A comprehensive resource of interacting protein regions for refining human transcription factor networks
Advanced Research Centers, Keio University, Yokohama, Japan
PLoS ONE 5:e9289. 2010
..Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function...
- Disease candidate gene identification and prioritization using protein interaction networks
Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
BMC Bioinformatics 10:73. 2009
..In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses...
- Structure-based prediction of protein-protein interactions on a genome-wide scale
Qiangfeng Cliff Zhang
Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
Nature 490:556-60. 2012
..The surprising effectiveness of three-dimensional structural information can be attributed to the use of homology models combined with the exploitation of both close and remote geometric relationships between proteins...
- Geometric de-noising of protein-protein interaction networks
Department of Computer Science, University of California, Irvine, California, USA
PLoS Comput Biol 5:e1000454. 2009
..The data and Matlab code implementing the methods are freely available from the web site: http://www.kuchaev.com/Denoising...
- PepX: a structural database of non-redundant protein-peptide complexes
VIB Switch Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
Nucleic Acids Res 38:D545-51. 2010
..Moreover, we provide an additional source of data for peptide design by annotating peptides with naturally occurring backbone variations using fragment clusters from the BriX database...
- COXPRESdb: a database to compare gene coexpression in seven model animals
Graduate School of Information Science, Tohoku University, 6 3 09 Aramaki Aza Aoba, Aoba ku, Sendai 980 8679, Japan
Nucleic Acids Res 39:D1016-22. 2011
..With the functions for gene network representation, COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species...
- BioNet: an R-Package for the functional analysis of biological networks
Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, 97074 Wurzburg, Germany
Bioinformatics 26:1129-30. 2010
..Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules...
- Computational approaches for detecting protein complexes from protein interaction networks: a survey
Institute for Infocomm Research, 1 Fusionopolis Way, Singapore
BMC Genomics 11:S3. 2010
..They can be used together with the experimental methods for mapping the interactions of proteins to understand how different proteins are organized into higher-level substructures to perform various cellular functions...
- Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
Benjamin A Shoemaker
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Nucleic Acids Res 38:D518-24. 2010
..IBIS is updated regularly and is freely accessible via http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html...
- Protein-protein docking with backbone flexibility
Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
J Mol Biol 373:503-19. 2007
..The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models...
- Evaluating contributions of natural language parsers to protein-protein interaction extraction
Department of Computer Science, University of Tokyo, Tokyo, Japan
Bioinformatics 25:394-400. 2009
..We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system...
- Protein-protein docking benchmark version 3.0
Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
Proteins 73:705-9. 2008
..0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark...
- 3did Update: domain-domain and peptide-mediated interactions of known 3D structure
Institute for Research in Biomedicine, Barcelona Supercomputing Center, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
Nucleic Acids Res 37:D300-4. 2009
..A web-based tool to query 3did is available at http://3did.irbbarcelona.org...
- AtPIN: Arabidopsis thaliana protein interaction network
Marcelo M Brandão
Departamento de Genetica, Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sao Paulo, 13400 970 Piracicaba, SP, Brazil
BMC Bioinformatics 10:454. 2009
..To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets...
- Proteome scanning to predict PDZ domain interactions using support vector machines
Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada
BMC Bioinformatics 11:507. 2010
..Once validated these predictions will help to increase the coverage of current PDZ domain interaction networks and further our understanding of the roles that PDZ domains play in a variety of biological processes...
- Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
Plant Cell 22:1264-80. 2010
..The obtained interaction map constitutes a framework for further in-depth analysis of the cell cycle machinery...
- DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions
Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield Ave, Detroit, MI 48201, USA
BMC Genomics 9:461. 2008
..No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster...
- ConsensusPathDB--a database for integrating human functional interaction networks
Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
Nucleic Acids Res 37:D623-8. 2009
..The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de...
- Protein-protein docking benchmark version 4.0
Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
Proteins 78:3111-4. 2010
..Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/...
- Docking and scoring protein interactions: CAPRI 2009
Marc F Lensink
Genome and Network Bioinformatics, CP 263, BC6, Universite Libre de Bruxelles, Blvd du Triomphe, 1050 Bruxelles, Belgium
Proteins 78:3073-84. 2010
- The landscape of human proteins interacting with viruses and other pathogens
Matthew D Dyer
Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
PLoS Pathog 4:e32. 2008
..Supplementary data accompanying this paper is available at http://staff.vbi.vt.edu/dyermd/publications/dyer2008a.html...