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V K MA, Chandrasekaran VM, Pandurangan S. Protein Domain Level Cancer Drug Targets in the Network of MAPK Pathways. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:2057-2065. [PMID: 29993692 DOI: 10.1109/tcbb.2018.2829507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins in the MAPK pathways considered as potential drug targets for cancer treatment. Pathways along with the cross-talks increase their scope to view them as a network of MAPK pathways. Side effect causing targeted domains act as a proxy for drug targets due to its structural similarity and frequent reuse of their variants. We proposed to identify non-repeatable protein domains as the drug targets to disrupt the signal transduction than targeting the whole protein. Network based approach is used to understand the contribution of 52 domains in non-hub, non-essential, and intra-pathway cancerous nodes and to identify potential drug target domains. 34 distinct domains in the cancerous proteins are playing vital roles in making cancer as a complex disease and pose challenges to identify potential drug targets. Distribution of domain families follows the power law in the network. Single promiscuous domains are contributing to the formation of hubs like Pkinease, Pkinease Tyr, and Ras. Hub nodes are positively correlated with the domain coverage and targeting them would disrupt functional properties of the proteins. EIF 4EBP, alpha Kinase, Sel1, ROKNT, and KH 1 are the domains identified as potential domain targets for the disruption of the signaling mechanism involved in cancer.
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Ribeiro AJM, Holliday GL, Furnham N, Tyzack JD, Ferris K, Thornton JM. Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites. Nucleic Acids Res 2019; 46:D618-D623. [PMID: 29106569 PMCID: PMC5753290 DOI: 10.1093/nar/gkx1012] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/13/2017] [Indexed: 12/28/2022] Open
Abstract
M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site.
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Affiliation(s)
- António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gemma L Holliday
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 1HT, UK
| | - Jonathan D Tyzack
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Katherine Ferris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Abstract
Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these are a vast number of databases for the more specialized user, dealing with specific families, diseases, structural features, and so on.
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Affiliation(s)
- Roman A Laskowski
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Lau CKY, Krewulak KD, Vogel HJ. Bacterial ferrous iron transport: the Feo system. FEMS Microbiol Rev 2015; 40:273-98. [PMID: 26684538 DOI: 10.1093/femsre/fuv049] [Citation(s) in RCA: 212] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 01/24/2023] Open
Abstract
To maintain iron homeostasis within the cell, bacteria have evolved various types of iron acquisition systems. Ferric iron (Fe(3+)) is the dominant species in an oxygenated environment, while ferrous iron (Fe(2+)) is more abundant under anaerobic conditions or at low pH. For organisms that must combat oxygen limitation for their everyday survival, pathways for the uptake of ferrous iron are essential. Several bacterial ferrous iron transport systems have been described; however, only the Feo system appears to be widely distributed and is exclusively dedicated to the transport of iron. In recent years, many studies have explored the role of the FeoB and FeoA proteins in ferrous iron transport and their contribution toward bacterial virulence. The three-dimensional structures for the Feo proteins have recently been determined and provide insight into the molecular details of the transport system. A highly select group of bacteria also express the FeoC protein from the same operon. This review will provide a comprehensive look at the structural and functional aspects of the Feo system. In addition, bioinformatics analyses of the feo operon and the Feo proteins have been performed to complement our understanding of this ubiquitous bacterial uptake system, providing a new outlook for future studies.
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Affiliation(s)
- Cheryl K Y Lau
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Karla D Krewulak
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
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Khazanov NA, Damm-Ganamet KL, Quang DX, Carlson HA. Overcoming sequence misalignments with weighted structural superposition. Proteins 2012; 80:2523-35. [PMID: 22733542 DOI: 10.1002/prot.24134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Revised: 06/05/2012] [Accepted: 06/10/2012] [Indexed: 11/09/2022]
Abstract
An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD's robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, secondary-structure matching, combinatorial extension, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics-scale analysis. HwRMSD can align homologs with low-sequence identity and large conformational differences, cases where both sequence-based and structural-based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence-alignment method, substitution matrix, and gap parameters for each unique pair of homologs.
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Affiliation(s)
- Nickolay A Khazanov
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
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6
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Abstract
Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these there are a vast number of databases for the most specialized user, dealing with specific families, diseases, structural features and so on.
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Laskowski RA. Protein structure databases. Methods Mol Biol 2010; 609:59-82. [PMID: 20221913 DOI: 10.1007/978-1-60327-241-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds--particularly useful for newly solved structures, and especially those of unknown function. Beyond these there are a vast number of databases for the more specialized user, dealing with specific families, diseases, structural features, and so on.
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Affiliation(s)
- Roman A Laskowski
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Le Roes-Hill M, Goodwin C, Burton S. Phenoxazinone synthase: what's in a name? Trends Biotechnol 2009; 27:248-58. [DOI: 10.1016/j.tibtech.2009.01.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 11/29/2022]
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Dobson PD, Patel Y, Kell DB. ‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries. Drug Discov Today 2009; 14:31-40. [DOI: 10.1016/j.drudis.2008.10.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 10/14/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
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Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. Arrangements in the modular evolution of proteins. Trends Biochem Sci 2008; 33:444-51. [PMID: 18656364 DOI: 10.1016/j.tibs.2008.05.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 05/28/2008] [Accepted: 05/28/2008] [Indexed: 11/17/2022]
Abstract
It has been known for the last couple of decades that proteins evolve partly through rearrangements of larger fragments, typically domains. These units are considered the basic modules of protein structure, evolution and function. In the last few years, the analysis of protein-domain rearrangements has provided us with functional and evolutionary insights and has aided improved functional predictions and domain assignments to previously uncharacterised genes and proteins. Although some mechanisms that govern modular rearrangements of protein domains have been uncovered, such as the addition or deletion of a single N- or C-terminal domain, much is still unknown about the genetics behind these arrangements.
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Affiliation(s)
- Andrew D Moore
- Evolutionary Bioinformatics, IEB, University of Münster, Hüfferstrasse 1, Münster, Germany
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Dobson PD, Kell DB. Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? Nat Rev Drug Discov 2008; 7:205-20. [PMID: 18309312 DOI: 10.1038/nrd2438] [Citation(s) in RCA: 325] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is generally thought that many drug molecules are transported across biological membranes via passive diffusion at a rate related to their lipophilicity. However, the types of biophysical forces involved in the interaction of drugs with lipid membranes are no different from those involved in their interaction with proteins, and so arguments based on lipophilicity could also be applied to drug uptake by membrane transporters or carriers. In this article, we discuss the evidence supporting the idea that rather than being an exception, carrier-mediated and active uptake of drugs may be more common than is usually assumed - including a summary of specific cases in which drugs are known to be taken up into cells via defined carriers - and consider the implications for drug discovery and development.
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Affiliation(s)
- Paul D Dobson
- School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Laskowski RA, Thornton JM. Understanding the molecular machinery of genetics through 3D structures. Nat Rev Genet 2008; 9:141-51. [PMID: 18160966 DOI: 10.1038/nrg2273] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Detailed knowledge of the three-dimensional structures of biological molecules has had an enormous impact on all areas of biological science, including genetics, as structure can reveal the fine details of how molecules perform their biological functions. Here we consider how changes in protein sequence affect the corresponding 3D structure, and describe how structural information about proteins, DNA and chromatin has shed light on gene regulatory mechanisms and the storage and transmission of epigenetic information. Finally, we describe how structure determination is benefiting from the high-throughput technologies of the worldwide structural genomics projects.
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Affiliation(s)
- Roman A Laskowski
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
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Abstract
Zinc is one of the metal ions essential for life, as it is required for the proper functioning of a large number of proteins. Despite its importance, the annotation of zinc-binding proteins in gene banks or protein domain databases still has significant room for improvement. In the present work, we compiled a list of known zinc-binding protein domains and of known zinc-binding sequence motifs (zinc-binding patterns), and then used them jointly to analyze the proteome of 57 different organisms to obtain an overview of zinc usage by archaeal, bacterial, and eukaryotic organisms. Zinc-binding proteins are an abundant fraction of these proteomes, ranging between 4% and 10%. The number of zinc-binding proteins correlates linearly with the total number of proteins encoded by the genome of an organism, but the proportionality constant of Eukaryota (8.8%) is significantly higher than that observed in Bacteria and Archaea (from 5% to 6%). Most of this enrichment is due to the larger portfolio of regulatory proteins in Eukaryota.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. BMC Evol Biol 2006; 6:91. [PMID: 17090320 PMCID: PMC1654190 DOI: 10.1186/1471-2148-6-91] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Accepted: 11/07/2006] [Indexed: 11/29/2022] Open
Abstract
Background The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. Results This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. Conclusion This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.
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Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJ. The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci 2006; 361:441-51. [PMID: 16524832 PMCID: PMC1609342 DOI: 10.1098/rstb.2005.1802] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.
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Affiliation(s)
- Keiran Fleming
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and MedicineLondon SW7 2AZ, UK
| | - Lawrence A Kelley
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and MedicineLondon SW7 2AZ, UK
- Biomolecular Modelling Laboratory, Cancer Research UK44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Suhail A Islam
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and MedicineLondon SW7 2AZ, UK
- Biomolecular Modelling Laboratory, Cancer Research UK44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Robert M MacCallum
- Biomolecular Modelling Laboratory, Cancer Research UK44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Arne Muller
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and MedicineLondon SW7 2AZ, UK
- Biomolecular Modelling Laboratory, Cancer Research UK44 Lincoln's Inn Fields, London WC2A 3PX, UK
| | - Florencio Pazos
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and MedicineLondon SW7 2AZ, UK
| | - Michael J.E Sternberg
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and MedicineLondon SW7 2AZ, UK
- Biomolecular Modelling Laboratory, Cancer Research UK44 Lincoln's Inn Fields, London WC2A 3PX, UK
- Author for correspondence ()
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Jones DT, Sternberg MJE, Thornton JM. Introduction. Bioinformatics: from molecules to systems. Philos Trans R Soc Lond B Biol Sci 2006; 361:389-91. [PMID: 16524827 PMCID: PMC1609343 DOI: 10.1098/rstb.2005.1811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- David T Jones
- University College London Department of Computer Science, Bioinformatics Unit Gower Street, London WC1E 6BT, UK
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