BIT: BioInformatics Tools أنظمة خادمة وأدوات في المعلوماتية الحيوية

Bioinformatics and Structural Biology - Tools & Services
		Relevant Publications & Communications: Dates: 2020 - 2019 - 2018 - 2017 - 2015 - 2014 - 2013 - 2012 - 2011 - 2009 - 2006 - 2005 - 2004 - 2003 - 2000 - 1999 - 1998 - 1997 See also: 2020 - Abdelkrim Rachedi Mutations in the SARS-CoV-2 complete genome sequences from strains isolated in Blida province, Algeria. JNBGP 2020: Journees Nationales virtuelles de bioinformatique: Genomique et proteomique - USDB, October 09-10, 2020 The contribution included the Viruses data Integration Database 2019 - Abdellahi Ould Ahmed Salem & Abdelkrim Rachedi^* Structural Targets Annotation Database - STAD & PR-Proteins selected targets. The International Conference on Biotechnology and Cancer, December 07-08, 2019 2019 - Soumeya KHERIS, Mokhtar BENREGUIEG and Abdelkrim RACHEDI* Bacterial Antibiotic Resistance Investigation Database - BARID. International Bioinformatics Day, JIBioinfo2019, 05 Nov. 2019 2018 - Abdellahi Ould Ahmed Salem, Mira Raimes, Aicha Bessaih, Mohamed Brahimi, Mohamed Amine Deghem, Mehdi Zein and Abdelkrim Rachedi* Structural & Functional Motifs in Metabolic Enzymes . A new set of Functional Motifs. 2^eme Colloques International, Biosciences 2108 "Genie Enzymatique et Production de Metabolites", 28-29 October2018, Oran, Algeria -> See: - Abstract -> - Conference Book: \|.1.\| or \|.2.\| 2018 - A. Rachedi, A. Mohammedi and A. Boukhalfa A Phytoecological Database for Annotating Flora in Region of Maamora - Saida, Algeria. Proceedings: International Seminar On Medicinal Plants (SIPM . January 2018), page 23., 2018, Al-Oued, Algeria ->See: Abstract 2017 - SALEM Abdellahi, RACHEDI Abdelkrim* Structural/Functional Motifs in the Enzymes of the Krebs Cycle, 1ER SEMINAIRE DE BIOINFORMATIQUE, April 04-06, 2017, Blida, Algeria. ->Explore: Citric Acid Cycle Binding Structural & Functional Motifs 2015 - Abdelkrim Rachedi. STAD the Structural Targets Annotation Database, Proceedings of the 08th International Biocuration Conference, From Big Data to Big Discovery April 23-26, 2015, Beijing, China. ->Find in Biocuration 2015 book 2014 - A Boukhalfa, A Mohammedi and A Rachedi An online Phytoecological Database and Exploration System for Flora in the region of Maamora, Saida., La Dynamique et la Valorisation des Ecocystemes Arides et Semi-arides dans un evironnement Changeant (DVEEC), Proceedings, page 59., 2014 2013 - Abdelkrim Rachedi. STAD: Structural Targets Annotation Database, Proceedings of the 11th International Conference on Biology and Synchrotron Radiation, 8 - 11 September 2013, Humburg, Germany. ( A conference Report has been published in the Journal Synchrotron Radiation, Volume 21, Part 1, Pages 280-282 January 2014, ->Find in Journal Synchrotron Radiation) 2013 - Abdelkrim Rachedi, Khuphukile Madida. NALD: Nucleic Acids and Ligands Database, Modeling Approaches and Algorithms for Advanced Computer Applications (Springer) 2013, 488: 329-336 ->Find in SpringerLink 2013 - Abdelkrim Rachedi. Vers une Base-de-donnees et System d'Exploitation en ligne de la Flore en Algerie (http://www.bioinformaticstools.org/fina). La Journee Scientifique Sur l'Eau et l'Environnement, 30 Juin 2013, Universite Dr. Tahar Moulay,Saida, Algerie. 2012 - Abdelkrim Rachedi and Wits University (Johannesburg) SYSTEMS AND METHODS FOR USE IN MOLECULAR DRUG DESIGN, Patent publication (WO2012/12043), 13 Sept. 2012. ->Find in WIPO 2012 - Abdelkrim Rachedi Bioinformatics in Diseases (like cancer, HIV, Malaria ... etc). International Seminar ' Cancer, Cellular Stress and Bioactive Substances' CSCSB, 23-24 September 2012 - Jijel, Algeria 2011 - Abdelkrim Rachedi, Khuphukile Madida. NALD: Nucleic Acids and Ligands Database; Ligand Binding Motifs, Binding Classes & Disease Links, 2nd ISCB Africa ASBCB Conference on Bioinformatics, March 9-11, 2011 - CapeTown, South Africa. 2011 - Abdelkrim Rachedi. Annotation of structural targets in SouthAfrica; the STAD database, 2nd ISCB Africa ASBCB Conference on Bioinformatics, March 9-11, 2011 - CapeTown, South Africa. 2009 - Abdelkrim Rachedi. STAD: Structural Targets Annotation Database, Proceedings for the Second Southern African Bioinformatics Workshop, 11th - 12th, Johannesburg, October 2009 - Johannesburg, South Africa. 2006 - Albeck S, .., Rachedi A et.al. SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr. 2006 Oct. ->Find in PubMed 2005 - (in relation to the SSFS system ) Golovin A., Dimitropoulos D., Oldfield T., Rachedi A. and Henrick (2005) MSDsite: A Database Search and Retrieval System for the Analysis and Viewing of Bound Ligands and Active Sites. PROTEINS: Structure, Function, and Bioinformatics 58(1): 190-9. ->Find in PubMed 2004 - A. Golovin, .., A. Rachedi et. al. E-MSD: an integrated data resource for bioinformatics, Nucleic Acids Research, 32 (Database issue), D211-D216, 2004. 2003 - Boutselakis, .., Rachedi, A. et. al. E-MSD: The European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Research, 31, 458-462, 2003. 2000 - Abdelkrim Rachedi, Michael Rebhan and Hong Xue. GABAagent: a system for integrating data on GABA receptors. Bioinformatics. 2000 Apr;16(4):301-12. ->Find in PubMed GABAagent and 3D-GDD databases have been featured under the NetWatch category (GABAing) in Science 287:5455 on February 11, 2000. See PDF: GABAing See also: news0527.pdf: HKUST Univ. press release about the GABAagent system. 1999 - Abdelkrim Rachedi, Michael Rebhan and Hong Xue. Internet-based Integrated Retrieval Information System for GABA receptors. Society for Neuroscience Abstracts. Vol.25, Part 2, page 1809, Oct. 1999 - Miami Beach, Florida, United States. 1999 - Khoo ASB, Balraj P, Rachedi A, Chin CN, Volpi L. A novel complex mutation of the OTC (Ornithine Transcarbamylase) Gene in a Malaysian Pedigree. Human Mutation. 1999 Nov; 14(5): 448. 1998 - Khoo ASB, Balraj P, Rachedi A, Volpi L., Chin CN. Clinical Correlation of a Novel Mutant Ornithine Transcarbamylase (OTCase) Homology Model. In Proceedings of the 10th National Biotechnology Seminar: Biotechnology towards the next millenium, pages 26-27. SIRIM Berhad, Malaysia, 27 & 28 October 1998. See link to the Proceedings: https://library.mosti.gov.my/cgi-bin/koha/opac-MARCdetail.pl?biblionumber=19413 See also: Clinical Correlation of a Novel Mutant Ornithine Transcarbamylase (OTCase) Homology Model 1998 - Khoo ASB, Balraj P, Rachedi A, Volpi L., Tan SK, Lim PKC, Chin CN. Molecular Genetic Investigations of a family with multiple early neonatal deaths. In Abstracts of the First Scientific Seminar of the National Institutes of Health, Ministry of Health, Malaysia: Research in the New Millenium, Page 45. Kuala Lumpur, Malaysia, 30-31 October 1998. 1997 - A. Rachedi, C.E. Sansom, C.R. Groom, J. Thillet, R. Griffin & A.J. Geddes. The Structure of Mouse Dihydrofolate Reductase in Ternary Complex with NADPH and the Lipophilic Antifolate, Methylbenzoprim. In Proceedings of the 9th National Biotechnology Seminar: Positioning National R & D in Biotechnology for Global Competitiveness, pages 96-102. Penang, Malaysia, 23-26 November 1997. See link to the Proceedings: https://library.mosti.gov.my/cgi-bin/koha/opac-MARCdetail.pl?biblionumber=19469 Dates: 2020 - 2019 - 2018 - 2017 - 2015 - 2014 - 2013 - 2012 - 2011 - 2009 - 2006 - 2005 - 2004 - 2003 - 2000 - 1999 - 1998 - 1997 Timeline ... April 2017: CACFMS Structural/Functional Motifs In The Enzymes Of The Krebs Cycle, by the SBB group at UTM Univ., Saida, Algeria. More... September 2015: CUPID A new online under-developement system comes as a result of international collaboration project with Dept. of Cell and Molecular Biology, Uppsala University,Uppsala,Sweden. More... November 2014: FIMA A new online Phytoecological Database & Exploration System for Flora in the region of Maamora, Saida, created by the SBB group at UTM Univ., Saida, Algeria. More... September 2014: STAD updates; 2 new Targets by the SBB group at UTM Univ., Saida, Algeria. More... January 2014: DIRC a newly created bioinformatics service tool for creating database systems providing integrated data for a set of biology-related keywords. More... December 2013: STAD updates; 9 new 3D structures by UCT Univ., South Africa and 3 updated targets by UAE Univ., Morocco. More... November 2013: Neuro. updates; a new card module (5^th), News card (RSS feed), has been added to the Neuro system”. More... September 2013: STAD updates; new structural targets More... August 2013: Neuro. system now provides a 4^th card of search results called Videos card”. More... August 2013: STAD updates; 4 new 3D structures of the Amidase enzyme by the Strcutural Biology Group, UCT Univ., Capetown, South Africa. More... June 2013: Neuro. system now provides 3 cards of search results. These include “Integrated Data”, “Disease” and “Sites & Images” cards. More... May 2013: NALD Database & Methods published in Springer. More... April 2013: "Neuro." updates; a new bioinformatics resource More... February 2013: STAD updates; new structural targets More... September 2012: Patent publication (WO2012/12043) "SYSTEMS AND METHODS FOR USE IN MOLECULAR DRUG DESIGN" More... February 2011: STAD the first and only African contributor to the PSI TargetTrack More... Bioinformatics news ... New details of SARS-COV-2 stru... Team uncovers new details of S... San Diego Supercomputer Center... Structural and functional char... PacBio Bioinformatics Focusing... IIT-BHU holds five-day course ... How Artist Angela Palmer Visua... Ultrafast structural changes d... Targeting Ras-binding domain o... Bioinformatics analysis of rhe... Bioinformatics Services Global... Accurate prediction by AlphaFo... Cryo-EM analyses of KIT and on... Molecular identification of th... Structural insight into the in... Structural basis and dynamics ... Researchers develop deeply int... Bioinformatics Market Size to ... Multiomic analysis of malignan... A new model predicts the flexi... From the journals: MCP - ASBMB... Pan-genome inversion index rev... Identification of a broadly co... Iowa State University undergra... New Fellowship Program Aims to... Using a long-read approach to ... IIT Madras researchers develop... Protein structure and folding ... The IPDGC/GP2 Hackathon - an o... Amity University organizes the... The symptoms of benign prostat... Muscle cell-type diversificati... Immunization of broiler chicke... Evolution of tetraspanin antig... Advancing structural biology t... Characterization of a novel pa... Different molecular pathways a... Development of novel broad-spe... Increasing the melting tempera... A contractile injection system... Genome-wide association study ... Double Dare: Exscientia Expand... Improving protein succinylatio... The effects of amino acid subs... Fiber Optic Gyroscopes Inclino... A Spark of recognition: Databr... The Bioteque: a computational ... Bioinformatics Global Market R... Pan-kinome of Legionella expan... Unfreezing waters in ligand bi... Andrew McLachlan (1935 – 202... Structure-informed microbial p... PacBio and the University of T... The structural basis for HIV-1... AlphaFold's new rival? Meta AI... 'New era in digital biology': ... A structural biology community... Structural basis of broad-spec... Editorial Article: The role of... Pangenomic analysis identifies... The Global Bioinformatics Mark... ISC Class 12 Biotechnology Syl... Some coronaviruses kill, while... A structural mechanism of nucl... Understanding Structural Biolo... Study identifies novel inhibit... Structural basis of template s... Chemical Computing Group and D... Prediction of effector protein... Structural characterization of... Structural basis of V-ATPase V... Autotrophic Biofilms Sustained... Addressing the pervasive scarc... In vivo single-molecule analys... Structural basis for lipid and... Arima Genomics Announces New P... Faculty invited to next Westwo... A young researcher strives to ... Structural studies of the phos... Molecular Science and Art With... What is a bioinformatics degre... Structural basis underlying th... The Global Bioinformatics Mark... AlphaFold2 models indicate tha... In situ structural analysis re... In silico analyses of Wnt1 nsS... Mutations in SARS-CoV-2 struct... Construction of a trio-based s... Determination of oligosacchari... Computational analysis of the ... A structural homology approach... Structural basis of transition... Using Flow Cytometry in Protei... Structural basis of tankyrase ... Structural basis for SHOC2 mod... Postdoctoral Position in Struc... A “best-in-class” systemic... Remembering St. Louis Individu... The SspB adaptor drives struct... Nanobodies and chemical cross-... National & International Conferences.. International conferences: Bioinformatics conferences Biotechnology conferences Biology conferences ConferenceAlerts: All fields conferences ScienceDz: All fields conferences National conferences: ConferenceAlerts: Algeria conferences ... 1 ConferenceAlerts: Algeria conferences ... 2 ScienceDz: Algeria conferences IEEE: Algeria conferences BIT's other services
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Tools, Databases & Services COVID-19 & Viruses Data Integration SARS-CoV-2 Variants, Genomes & Mutations Explorer Viruses Integration Database (Incl. SARS-CoV-2) Vr-β ^{[6], [8]} Bioinformatics Mobile Apps. FIMA Android vr 1.0 ^{[4.1], [4.2]} GABAagent Android vr 1.0 ^[6] Microbial Bioinformatics Research & Services BARID: Bacterial Antibiotic Resistance Investigation Database ^[7] Structural Bioinformatics Research & Services SSFS: Sequence, Structure and Function Server ^[1] STAD: Structural Targets Annotation Database ^{[2.1], [2.2], [2.3], [2.4], [2.5], [2.6]} - See also: NALD: Nucleic Acids and Ligands Database ^[3] Flora Annotation FIMA: Flora in Maamora, Saida, Algeria ^{[4.1], [4.2]} FINA: Flora in Algeria, Database ^[5] Data Intergation tools and databases DIRC: A system for creating data integrated databases and search tools for biology-related topics CUPID:Chaperone/Usher Pathway Identification Database GABAagent: A system for integrating data on GABA receptors ^[6] EblRsr: A resource system for integrating data on the Ebola Virus Disease and related topics. Genomics N2PR: Nucleic Acid Codes Translation to Proteins and Reverse
References ¹ 2005: Golovin A., Dimitropoulos D., Oldfield T., Rachedi A. and Henrick "MSDsite: A Database Search and Retrieval System for the Analysis and Viewing of Bound Ligands and Active Sites. PROTEINS: Structure, Function, and Bioinformatics 58(1): 190-9 2005" << Find in PubMed ⁸2020: Abdelkrim Rachedi Mutations in the SARS-CoV-2 complete genome sequences from strains isolated in Blida province, Algeria. JNBGP 2020: Journees Nationales virtuelles de bioinformatique: Genomique et proteomique - USDB, October 09-10, 2020 ⁷ 2019: Soumeya KHERIS, Mokhtar BENREGUIEG and Abdelkrim RACHEDI* Bacterial Antibiotic Resistance Investigation Database - BARID. International Bioinformatics Day, JIBioinfo2019, 05 Nov. 2019 ^2.1 2019: Abdellahi Ould Ahmed Salem & Abdelkrim Rachedi^*Structural Targets Annotation Database - STAD & PR-Proteins selected targets, The International Conference on Biotechnology and Cancer, December 07-08, 2019 - Oran, Algeria.->Find in Conference Book ^2.2 2015: Abdelkrim Rachedi. STAD the Structural Targets Annotation Database, Proceedings of the 08th International Biocuration Conference, From Big Data to Big Discovery, April 23-26,2015 - Beijing, China. ^2.3 2013: Abdelkrim Rachedi. STAD: Structural Targets Annotation Database, Proceedings of the 11th International Conference on Biology and Synchrotron Radiation, 8 - 11 September 2013, Humburg, Germany. (A conference Report has been published in the Journal Synchrotron Radiation, Volume 21, Part 1, Pages 280-282 January 2014 ->Find in Journal Synchrotron Radiation) ^2.4 2011: Abdelkrim Rachedi. Annotation of structural targets in South Africa; the STAD database, 2nd ISCB Africa ASBCB Conference on Bioinformatics, March 9-11, 2011 - CapeTown, South Africa. ^2.5 2009: Abdelkrim Rachedi. STAD: Structural Targets Annotation Database, Proceedings for the Second Southern African Bioinformatics Workshop, 11th - 12th, Johannesburg, October 2009 - Johannesburg, South Africa. ^2.6 2006: Albeck S, ..,Rachedi A. .., Henrick K. "SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr. 2006 ->Find in PubMed ³ 2013: Abdelkrim Rachedi, Khuphukile Madida. NALD: Nucleic Acids and Ligands Database, Modeling Approaches and Algorithms for Advanced Computer Applications (Springer) 2013, 488: 329-336 ->Find in SpringerLink ^4.1 2018: A. Rachedi, A. Mohammedi and A. Boukhalfa, A Mohammedi A Phytoecological Database for Annotating Flora in Region of Maamora - Saida, Algeria. Proceedings: International Seminar On Medicinal Plants (SIPM . 2018), page 23., 2018 ^4.2 2014: A Boukhalfa, A Mohammedi and A Rachedi. An online Phytoecological Database and Exploration System for Flora in the region of Maamora, Saida, La Dynamique et la Valorisation des Ecocystemes Arides et Semi-arides dans un evironnement Changeant (DVEEC), Proceedings, page 59., 2014 ⁵ 2013: Abdelkrim Rachedi. Vers une Base-de-donnees et System d'Exploitation en ligne de la Flore en Algerie (http://www.bioinformaticstools.org/fina). La Journee Scientifique Sur l'Eau et l'Environnement, 30 Juin 2013, Universite Dr. Tahar Moulay,Saida, Algerie. ⁶ 2000: Abdelkrim Rachedi, Michael Rebhan and Hong Xue. GABAagent: a system for integrating data on GABA receptors. Bioinformatics. 2000 Apr;16(4):301-12. ->Find in PubMed
Contact: Dr. Abdelkrim Rachedi at rachedi@bioinformaticstools.org - © 2011-2021

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