Engineering Proteins from Sequence Statistics: Identifying and Understanding the Roles
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Perspectives on Supercomputing and Artificial Intelligence Applications In
DOI: 10.14529/jsfi200302 Perspectives on Supercomputing and Artificial Intelligence Applications in Drug Discovery Jun Xu1,2, Jiming Ye1 c The Authors 2020. This paper is published with open access at SuperFri.org This review starts with outlining how science and technology evaluated from last century into high throughput science and technology in modern era due to the Nobel-Prize-level inventions of combinatorial chemistry, polymerase chain reaction, and high-throughput screening. The evolu- tion results in big data accumulated in life sciences and the fields of drug discovery. The big data demands for supercomputing in biology and medicine, although the computing complexity is still a grand challenge for sophisticated biosystems in drug design in this supercomputing era. In or- der to resolve the real-world issues, artificial intelligence algorithms (specifically machine learning approaches) were introduced, and have demonstrated the power in discovering structure-activity relations hidden in big biochemical data. Particularly, this review summarizes on how people mod- ernize the conventional machine learning algorithms by combing non-numeric pattern recognition and deep learning algorithms, and successfully resolved drug design and high throughput screening issues. The review ends with the perspectives on computational opportunities and challenges in drug discovery by introducing new drug design principles and modeling the process of packing DNA with histones in micrometer scale space, an example of how a macrocosm object gets into microcosm world. Keywords: drug discovery, big data, artificial intelligence, HPC. 1. Big Data and Supercomputing Challenges in Drug Discovery In the last century, three cutting-edge inventions, which were combinatorial chemistry (CC), polymerase chain reaction (PCR), and high-throughput screening (HTS), significantly changed biomedical science and technology. -
Ancient Metaproteomics: a Novel Approach for Understanding Disease And
Ancient metaproteomics: a novel approach for understanding disease and diet in the archaeological record Jessica Hendy PhD University of York Archaeology August, 2015 ii Abstract Proteomics is increasingly being applied to archaeological samples following technological developments in mass spectrometry. This thesis explores how these developments may contribute to the characterisation of disease and diet in the archaeological record. This thesis has a three-fold aim; a) to evaluate the potential of shotgun proteomics as a method for characterising ancient disease, b) to develop the metaproteomic analysis of dental calculus as a tool for understanding both ancient oral health and patterns of individual food consumption and c) to apply these methodological developments to understanding individual lifeways of people enslaved during the 19th century transatlantic slave trade. This thesis demonstrates that ancient metaproteomics can be a powerful tool for identifying microorganisms in the archaeological record, characterising the functional profile of ancient proteomes and accessing individual patterns of food consumption with high taxonomic specificity. In particular, analysis of dental calculus may be an extremely valuable tool for understanding the aetiology of past oral diseases. Results of this study highlight the value of revisiting previous studies with more recent methodological approaches and demonstrate that biomolecular preservation can have a significant impact on the effectiveness of ancient proteins as an archaeological tool for this characterisation. Using the approaches developed in this study we have the opportunity to increase the visibility of past diseases and their aetiology, as well as develop a richer understanding of individual lifeways through the production of molecular life histories. iii iv List of Contents Abstract ............................................................................................................................... -
Backbone Dynamics of Free Barnase and Its Complex with Barstar Determined by 15N NMR Relaxation Study
Journal of Biomolecular NMR, 18: 107–118, 2000. KLUWER/ESCOM 107 © 2000 Kluwer Academic Publishers. Printed in the Netherlands. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study Sarata C. Sahua, Abani K. Bhuyanb, Jayant B. Udgaonkarb & R.V. Hosura;∗ aDepartment of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India; bNational Centre for Biological Sciences, Tata Institute of Fundamental Research, University of Agricultural Sciences (UAS) - Gandhi Krishi Vigyan Kendra (GKVK) Campus, Bangalore 560 065, India Received 18 April 2000; Accepted 7 July 2000 Key words: backbone dynamics, barnase, barstar, complex, 15N NMR relaxation, protein–protein interactions Abstract Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 ◦C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D {1H}-15N NMR spec- 15 troscopy. N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear {1H}-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N- terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (τm) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. -
Characterization of in Vitro Oxidized Barstar
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector FEBS 15911 FEBS Letters 370 (1995) 273-277 Characterization of in vitro oxidized barstar C. Frisch, G. Schreiber, A.R. Fersht* Cambridge Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge, CB2 2QH, UK Received 13 July 1995 mutant which has been solved independently by Guillet et al. Abstract The polypeptide inhibitor of the ribonuclease barnase, [8] to 2.6 A resolution and by Buckle et al. [4] to 2.0/k resolu- barstar, has two cysteine residues in positions 40 and 82. These tion. The distance between the s-carbon atoms of the alanines have been proposed to form a disulfide bridge leading to an in position 40 and 82 in the two crystal structures of the barstar increase in stability without changing the inhibitory activity of the protein. Barstar and a mutant (E80A) were oxidized in vitro and (C40A/C82A) double mutant is 11.4 A [8] and 11.7 A [4], re- the biochemical and physico-chemical properties of the oxidized spectively. In the solution structure of barstar that was deter- monomers were analysed. The oxidized proteins show no inhibi- mined by NMR [7] (Fig. 1), the distance between the s-carbon tion of barnase using a plate assay and are significantly destabi- atoms of the cysteines is 11.5 h. These s-carbon distances are lized. CD spectra indicate a loss of secondary structure. The outside the normal range for a disulfide bond, which is usually amino acid substitution E80 --~ A stabilizes the oxidized barstar from 4.4 to 6.8 A [9]. -
The TIM Barrel Fold Nagarajan D
The TIM barrel fold Nagarajan D. and Nanajkar N. Comments and corrections: Line 10: fix “αhelices” in “α-helices”. Lines 11-12: C-terminal loops are important for catalytic activity, while N-terminal loops are important for the stability of the TIM-barrels. This should be mentioned. Line 14: The reference #7 is not related to the statement. Line 14: There is a new EC classe (EC.7, translocases). Change “5 of 6” in “5 of 7”. Lines 26-27: It is not correct to state that the shear number of 8 for the TIM-barrels is due to “their staggered nature”. Most of the β-barrels have a staggered nature, but their shear number is not 8. Line 27: The reference #2 is imprecise. Wierenga did not defined himself the shear number of TIM-barrel proteins. Please check the 2 papers of Murzin AG, 1994, “Principle determining the structure of β-sheet barrels in proteins,” I and II, and the paper of Liu W, 1998, “Shear numbers of protein β-barrels: definition refinements and statistics”. Line 29: Again, it is not correct to state that the 4-fold geometric symmetry depends on the stagger. Since the number of strands (n) is equal to the Shear number (S), side-chains point alternatively towards the pore and the core, giving a 4-fold symmetry. Line 37: “historically” is a bit exaggerated for a reference dated 2015, especially if it comes from the author itself. Find a true historic reference, or just mention that you defined the regions “core” and “pore”. Line 43: “Consequently” is misleading. -
Southwest Retort
SOUTHWEST RETORT SIXTY-NINTH YEAR OCTOBER 2016 Published for the advancement of Chemists, Chemical Engineers and Chemistry in this area published by The Dallas-Fort Worth Section, with the cooperation of five other local sections of the American Chemical Society in the Southwest Region. Vol. 69(2) OCTOBER 2016 Editorial and Business Offices: Contact the Editor for subscription and advertisement information. Editor: Connie Hendrickson: [email protected] Copy Editor: Mike Vance, [email protected] Business Manager: Danny Dunn: [email protected] The Southwest Retort is published monthly, September through May, by the Dallas-Ft. Worth Section of the American Chemical Society, Inc., for the ACS Sections of the Southwest Region. October 2016 Southwest RETORT 1 TABLE OF CONTENTS Employment Clearing House………….......3 Fifty Years Ago……………………….….....6 ARTICLES and COLUMNS Schulz Award Winner Gale Hunt………….7 And Another Thing……………………….11 Around the Area………………………….14 Letter from the Editor….…..……….........17 SPECIAL EVENTS National Chemistry Week…………………9 NEWS SHORTS Former pesticide ingredient found in dolphins, birds and fish……………………8 Coffee-infused foam removes lead from contaminated water………………………10 Snake venom composition could be related to hormones and diet……………………..13 Detecting blood alcohol content with an electronic skin patch………………...……16 INDEX OF ADVERTISERS Huffman Laboratories……………....……..4 Contact the DFW Section Vance Editing…..…………….…….……….4 General: [email protected] UT Arlington………………………………..4 Education: [email protected] ANA-LAB……………………...….…...……5 Elections: [email protected] Facebook: DFWACS Twitter: acsdfw October 2016 Southwest RETORT 2 EMPLOYMENT CLEARING HOUSE Job applicants should send name, email, and phone, along with type of position and geographical area desired; employers may contact job applicants directly. -
Smurflite: Combining Simplified Markov Random Fields With
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone Noah M. Daniels 1, Raghavendra Hosur 2, Bonnie Berger 2∗, and Lenore J. Cowen 1∗ 1Department of Computer Science, Tufts University, Medford, MA 02155 2Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139 ABSTRACT are limited in their power to recognize remote homologs because of Motivation: One of the most successful methods to date for their inability to model statistical dependencies between amino-acid recognizing protein sequences that are evolutionarily related has residues that are close in space but far apart in sequence (Lifson and been profile Hidden Markov Models (HMMs). However, these models Sander (1980); Zhu and Braun (1999); Olmea et al. (1999); Cowen do not capture pairwise statistical preferences of residues that are et al. (2002); Steward and Thorton (2002)). hydrogen bonded in beta sheets. These dependencies have been For this reason, many have suggested (White et al. (1994); partially captured in the HMM setting by simulated evolution in the Lathrop and Smith (1996); Thomas et al. (2008); Liu et al. (2009); training phase and can be fully captured by Markov Random Fields Menke et al. (2010); Peng and Xu (2011)) that more powerful (MRFs). However, the MRFs can be computationally prohibitive when Markov Random Fields (MRFs) be used. MRFs employ an auxiliary beta strands are interleaved in complex topologies. dependency graph which allows them to model more complex We introduce SMURFLite, a method that combines both simplified statistical dependencies, including statistical dependencies that Markov Random Fields and simulated evolution to substantially occur between amino-acid residues that are hydrogen bonded in beta improve remote homology detection for beta structures. -
The Grand Challenges in the Chemical Sciences
The Israel Academy of Sciences and Humanities Celebrating the 70 th birthday of the State of Israel conference on THE GRAND CHALLENGES IN THE CHEMICAL SCIENCES Jerusalem, June 3-7 2018 Biographies and Abstracts The Israel Academy of Sciences and Humanities Celebrating the 70 th birthday of the State of Israel conference on THE GRAND CHALLENGES IN THE CHEMICAL SCIENCES Participants: Jacob Klein Dan Shechtman Dorit Aharonov Roger Kornberg Yaron Silberberg Takuzo Aida Ferenc Krausz Gabor A. Somorjai Yitzhak Apeloig Leeor Kronik Amiel Sternberg Frances Arnold Richard A. Lerner Sir Fraser Stoddart Ruth Arnon Raphael D. Levine Albert Stolow Avinoam Ben-Shaul Rudolph A. Marcus Zehev Tadmor Paul Brumer Todd Martínez Reshef Tenne Wah Chiu Raphael Mechoulam Mark H. Thiemens Nili Cohen David Milstein Naftali Tishby Nir Davidson Shaul Mukamel Knut Wolf Urban Ronnie Ellenblum Edvardas Narevicius Arieh Warshel Greg Engel Nathan Nelson Ira A. Weinstock Makoto Fujita Hagai Netzer Paul Weiss Oleg Gang Abraham Nitzan Shimon Weiss Leticia González Geraldine L. Richmond George M. Whitesides Hardy Gross William Schopf Itamar Willner David Harel Helmut Schwarz Xiaoliang Sunney Xie Jim Heath Mordechai (Moti) Segev Omar M. Yaghi Joshua Jortner Michael Sela Ada Yonath Biographies and Abstracts (Arranged in alphabetic order) The Grand Challenges in the Chemical Sciences Dorit Aharonov The Hebrew University of Jerusalem Quantum Physics through the Computational Lens While the jury is still out as to when and where the impressive experimental progress on quantum gates and qubits will indeed lead one day to a full scale quantum computing machine, a new and not-less exciting development had been taking place over the past decade. -
Annual Report 2010 © Copyright 2011
Centre for Genomic Regulation Annual Report 2010 © Copyright 2011 Produced by: Department of Communication & Public Relations Centre for Genomic Regulation (CRG) Dr. Aiguader, 88 08003 Barcelona, Spain www.crg.eu Texts and graphics: CRG Researchers, Department of Communication and Public Relations Graphic Design: Genoma ArtStudio SCP (www.genoma-artstudio.com) Photography: Ivan Martí Printing: Novoprint, S.A. Legal deposit: B-24966-2011 CONTENTS CRG Scientific Structure 6 CRG Core Facilities Structure 8 CRG Management Structure 10 CRG Scientific Advisory Board (SAB) 12 CRG Business Board 13 Year Retrospect by the Director of the CRG: Miguel Beato 14 Research Programmes Gene Regulation 16 > Chromatin and gene expression 18 > Regulation of alternative pre-mRNA splicing during cell differentiation, development and disease 22 > Regulation of protein synthesis in eukaryotes 26 > Translational control of gene expression 29 Differentiation and Cancer 34 > Hematopoietic differentiation and stem cell biology 36 > Reprogramming and regeneration 40 > Epigenetics events in cancer 43 > Epithelial homeostasis and cancer 48 > Mechanisms of cancer and aging 51 Genes and Disease 54 > Genetic causes of disease 56 > Gene therapy 65 > Gene Function and murine models of disease 69 > Neurobehavioral phenotyping of mouse models of disease 73 > Genomic and epigenomic variation in disease 77 Bioinformatics and Genomics 82 > Bioinformatics and genomics 84 > Comparative bioinformatics 92 > Comparative genomics 96 > Evolutionary genomics 101 > Gene function and evolution -
The Medical & Scientific Library of W. Bruce
The Medical & Scientific Library of W. Bruce Fye New York I March 11, 2019 The Medical & Scientific Library of W. Bruce Fye New York | Monday March 11, 2019, at 10am and 2pm BONHAMS LIVE ONLINE BIDDING IS INQUIRIES CLIENT SERVICES 580 Madison Avenue AVAILABLE FOR THIS SALE New York Monday – Friday 9am-5pm New York, New York 10022 Please email bids.us@bonhams. Ian Ehling +1 (212) 644 9001 www.bonhams.com com with “Live bidding” in Director +1 (212) 644 9009 fax the subject line 48 hrs before +1 (212) 644 9094 PREVIEW the auction to register for this [email protected] ILLUSTRATIONS Thursday, March 7, service. Front cover: Lot 188 10am to 5pm Tom Lamb, Director Inside front cover: Lot 53 Friday, March 8, Bidding by telephone will only be Business Development Inside back cover: Lot 261 10am to 5pm accepted on a lot with a lower +1 (917) 921 7342 Back cover: Lot 361 Saturday, March 9, estimate in excess of $1000 [email protected] 12pm to 5pm REGISTRATION Please see pages 228 to 231 Sunday, March 10, Darren Sutherland, Specialist IMPORTANT NOTICE for bidder information including +1 (212) 461 6531 12pm to 5pm Please note that all customers, Conditions of Sale, after-sale [email protected] collection and shipment. All irrespective of any previous activity SALE NUMBER: 25418 with Bonhams, are required to items listed on page 231, will be Tim Tezer, Junior Specialist complete the Bidder Registration transferred to off-site storage +1 (917) 206 1647 CATALOG: $35 Form in advance of the sale. -
Decelerated Genome Evolution in Modern Vertebrates Revealed by Analysis of Multiple Lancelet Genomes
ARTICLE Received 20 May 2014 | Accepted 18 Nov 2014 | Published 19 Dec 2014 DOI: 10.1038/ncomms6896 OPEN Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes Shengfeng Huang1, Zelin Chen1, Xinyu Yan1, Ting Yu1, Guangrui Huang1, Qingyu Yan1, Pierre Antoine Pontarotti2, Hongchen Zhao1, Jie Li1, Ping Yang1, Ruihua Wang1, Rui Li1, Xin Tao1, Ting Deng1, Yiquan Wang3,4, Guang Li3,4, Qiujin Zhang5, Sisi Zhou1, Leiming You1, Shaochun Yuan1, Yonggui Fu1, Fenfang Wu1, Meiling Dong1, Shangwu Chen1 & Anlong Xu1,6 Vertebrates diverged from other chordates B500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. 1 State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. 2 Evolution Biologique et Mode´lisation UMR 7353 Aix Marseille Universite´/CNRS, 3 Place Victor Hugo, 13331 Marseille, France. -
EYAL AKIVA, Phd
Eyal Akiva CV, Nov. 2017 EYAL AKIVA, PhD Department of Bioengineering and Therapeutic Sciences Phone +1-650-504-9008 University of California at San Francisco Email [email protected] 1700 4th street, San Francisco, Web www.babbittlab.ucsf.edu/eakiva CA, USA EDUCATION 2012-2017 Post-doctoral fellowship at UCSF, Dept. Of Bioengineering and Therapeutic Sciences. Host: Prof. Patricia Babbitt. 2010-2012 Post-doctoral fellowship at UCSF, Dept. Of Bioengineering and Therapeutic Sciences. Host: Prof. Tanja Kortemme. 2004-2010 PhD at The Hebrew University of Jerusalem (Israel), bioinformatics. Host: Prof. Hanah Margalit. “Various Aspects of Modularity in Protein-Protein Interaction". 2001-2004 MSc at The Hebrew University of Jerusalem (Israel), bioinformatics and human genetics. Host: Prof. Muli Ben-Sasson. “Exploiting the Exploiters: Identification of Virus-Host Pep- tide Mimicry as a Source for Modules of Functional Significance”. MAGNA CUM LAUDE. 1997-2000 BSc at Bar-Ilan University (Israel), biology (major) and computer science (minor). Final project advisor: Prof. Ramit Mehr “Modeling the Evolution of the Immune System: a Sim- ulation of the Evolution of Genes that Encode the Variable Regions of Immunoglobulins”. MAGNA CUM LAUDE. 1996-1997 First year of "Industrial Engineering and Management" studies, Tel-Aviv University, Israel. OTHER WORK EXPERIENCE 2000-01 ‘Do-coop technologies’: Team leader and chemistry/microbiology researcher; development of biological applications and manufacture of proprietary nanoparticles (Or Yehuda, Israel and Tel-Aviv University (Prof. Eshel Ben-Jacob’s lab at the school of physics)). FUNDING, HONORS AND AWARDS 2017 Grant: Co-PI, “Utilizing metagenomic sequences for enzyme function prediction”, Joint Genome Institute (US Department of Energy) (http://jgi.doe.gov/doe-user-facilities-ficus- join-forces-to-tackle-biology-big-data/).