Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens
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MODELLER 10.1 Manual
MODELLER A Program for Protein Structure Modeling Release 10.1, r12156 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/03/12 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
User Guide of Computational Facilities
Physical Chemistry Unit Departament de Quimica User Guide of Computational Facilities Beta Version System Manager: Marc Noguera i Julian January 20, 2009 Contents 1 Introduction 1 2 Computer resources 2 3 Some Linux tools 2 4 The Cluster 2 4.1 Frontend servers . 2 4.2 Filesystems . 3 4.3 Computational nodes . 3 4.4 User’s environment . 4 4.5 Disk space quota . 4 4.6 Data Backup . 4 4.7 Generation of SSH keys for automatic SSH login . 4 4.8 Submitting jobs to the cluster . 5 4.8.1 Typical queue system commands . 6 4.8.2 HomeMade scripts . 6 4.8.3 Create your own submit script . 6 4.8.4 Submitting Parallel Calculations . 7 5 Available Software 9 5.1 Chemisty software . 9 5.2 Development Software . 10 5.3 How to use the software . 11 5.4 Non-default environments . 11 6 Your Linux Workstation 11 6.1 Disk space on your workstation . 12 6.2 Workstation Data Backup . 12 6.3 Running virtual Windows XP . 13 6.3.1 The Windows XP Environment . 13 6.4 Submitting calculations to your dekstop . 13 6.5 Network dependent structure . 14 7 Your WindowsXP Workstation 14 7.1 Workstation Data Backup . 14 8 Frequently asked questions 14 1 Introduction This User Guide is aimed to the standard user of the computer facilities in the ”Unitat de Quimica Fisica” in the Universitat Autnoma de Barcelona. It is not assumed that you have a knowledge of UNIX/Linux. However, you are 1 encouraged to take a close look to the linux guides that will be pointed out. -
Ranking of Substances for Monitoring in Foods, Drinks and Dietary Supplements - Based on Risk and Knowledge Gaps
VKM Report 2019: 13 Ranking of substances for monitoring in foods, drinks and dietary supplements - based on risk and knowledge gaps Scientific Opinion of the Scientific Steering Committee of the Norwegian Scientific Committee for Food and Environment Scientific Opinion of the Scientific Steering Committee of the Norwegian Scientific Committee for Food and Environment 16.09.2019 ISBN: 978-82-8259-329-8 ISSN: 2535-4019 Norwegian Scientific Committee for Food and Environment (VKM) Po 222 Skøyen N – 0213 Oslo Norway Phone: +47 21 62 28 00 Email: [email protected] vkm.no vkm.no/english Cover photo: Brace Suggested citation: VKM, Inger-Lise Steffensen, Christiane Kruse Fæste, Trine Husøy, Helle Katrine Knutsen, Gro Haarklou Mathisen, Robin Ørnsrud, Angelika Agdestein, Johanna Bodin, Edel Elvevoll, Dag O. Hessen, Merete Hofshagen, Åshild Krogdahl, Asbjørn Magne Nilsen, Trond Rafoss, Taran Skjerdal, Gaute Velle, Yngvild Wasteson, Gro-Ingunn Hemre, Vigdis Vandvik, Jan Alexander (2019). Ranking of substances for monitoring in foods, drinks and dietary supplements - based on risk and knowledge gaps. Scientific Opinion of the Scientific Steering Committee of the Norwegian Scientific Committee for Food and Environment. VKM report 2019:13, ISBN: 978-82-8259-329-8, ISSN: 2535-4019. VKM Report 2019: 13 Ranking of substances for monitoring in foods, drinks and dietary supplements - based on risk and knowledge gaps Preparation of the opinion The Norwegian Scientific Committee for Food and Environment (Vitenskapskomiteen for mat og miljø, VKM) appointed a project group to answer the request from the Norwegian Food Safety Authority. The project group consisted of six VKM members and a project leader from the VKM secretariat. -
Pyplif HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors
molecules Article PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors Enade P. Istyastono 1,* , Nunung Yuniarti 2, Vivitri D. Prasasty 3 and Sudi Mungkasi 4 1 Faculty of Pharmacy, Sanata Dharma University, Yogyakarta 55282, Indonesia 2 Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; [email protected] 3 Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia; [email protected] 4 Department of Mathematics, Faculty of Science and Technology, Sanata Dharma University, Yogyakarta 55282, Indonesia; [email protected] * Correspondence: [email protected]; Tel.: +62-274883037 Abstract: Identification of molecular determinants of receptor-ligand binding could significantly increase the quality of structure-based virtual screening protocols. In turn, drug design process, especially the fragment-based approaches, could benefit from the knowledge. Retrospective virtual screening campaigns by employing AutoDock Vina followed by protein-ligand interaction finger- printing (PLIF) identification by using recently published PyPLIF HIPPOS were the main techniques used here. The ligands and decoys datasets from the enhanced version of the database of useful de- coys (DUDE) targeting human G protein-coupled receptors (GPCRs) were employed in this research since the mutation data are available and could be used to retrospectively verify the prediction. The results show that the method presented in this article could pinpoint some retrospectively verified molecular determinants. The method is therefore suggested to be employed as a routine in drug Citation: Istyastono, E.P.; Yuniarti, design and discovery. N.; Prasasty, V.D.; Mungkasi, S. PyPLIF HIPPOS-Assisted Prediction Keywords: PyPLIF HIPPOS; AutoDock Vina; drug discovery; fragment-based; molecular determi- of Molecular Determinants of Ligand Binding to Receptors. -
Alternaria Alternata Toxins Synergistically Activate the Aryl Hydrocarbon Receptor Pathway in Vitro
biomolecules Article Alternaria alternata Toxins Synergistically Activate the Aryl Hydrocarbon Receptor Pathway In Vitro Julia Hohenbichler 1 , Georg Aichinger 1 , Michael Rychlik 2 , Giorgia Del Favero 1 and Doris Marko 1,* 1 Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Italy; [email protected] (J.H.); [email protected] (G.A.); [email protected] (G.D.F.) 2 Chair of Analytical Chemistry, Technical University of Munich, 80333 Munich, Germany; [email protected] * Correspondence: [email protected] Received: 18 June 2020; Accepted: 30 June 2020; Published: 9 July 2020 Abstract: Alternaria molds simultaneously produce a large variety of mycotoxins, of which several were previously reported to induce enzymes of phase I metabolism through aryl hydrocarbon receptor activation. Thus, we investigated the potential of naturally occurring Alternaria toxin mixtures to induce Cytochrome P450 (CYP) 1A1/1A2/1B1 activity. Two variants of an extract from cultured Alternaria alternata, as well as the toxins alternariol (AOH), alternariol monomethyl ether (AME), altertoxin I (ATX-I), and altertoxin II (ATX-II), were tested singularly and in binary mixtures applying the 7-ethoxy-resorufin-O-deethylase (EROD) assay in MCF-7 breast cancer cells. Sub-cytotoxic concentrations of the two toxin mixtures, as well as ATX-I, ATX-II and AOH, exhibited dose-dependent enhancements of CYP 1 activity. ATX-I and ATX-II interacted synergistically in this respect, demonstrating the two perylene quinones as major contributors to the extract’s potential. Binary mixtures between AOH and the two altertoxins respectively exhibited concentration-dependent antagonistic as well as synergistic combinatory effects. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
GROMACS: Fast, Flexible, and Free
GROMACS: Fast, Flexible, and Free DAVID VAN DER SPOEL,1 ERIK LINDAHL,2 BERK HESS,3 GERRIT GROENHOF,4 ALAN E. MARK,4 HERMAN J. C. BERENDSEN4 1Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden 2Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-10691 Stockholm, Sweden 3Max-Planck Institut fu¨r Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany 4Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands Received 12 February 2005; Accepted 18 March 2005 DOI 10.1002/jcc.20291 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simula- tions. The package includes about 100 utility and analysis programs. -
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
processes Review Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Outi M. H. Salo-Ahen 1,2,* , Ida Alanko 1,2, Rajendra Bhadane 1,2 , Alexandre M. J. J. Bonvin 3,* , Rodrigo Vargas Honorato 3, Shakhawath Hossain 4 , André H. Juffer 5 , Aleksei Kabedev 4, Maija Lahtela-Kakkonen 6, Anders Støttrup Larsen 7, Eveline Lescrinier 8 , Parthiban Marimuthu 1,2 , Muhammad Usman Mirza 8 , Ghulam Mustafa 9, Ariane Nunes-Alves 10,11,* , Tatu Pantsar 6,12, Atefeh Saadabadi 1,2 , Kalaimathy Singaravelu 13 and Michiel Vanmeert 8 1 Pharmaceutical Sciences Laboratory (Pharmacy), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland; ida.alanko@abo.fi (I.A.); rajendra.bhadane@abo.fi (R.B.); parthiban.marimuthu@abo.fi (P.M.); atefeh.saadabadi@abo.fi (A.S.) 2 Structural Bioinformatics Laboratory (Biochemistry), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland 3 Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; [email protected] 4 Swedish Drug Delivery Forum (SDDF), Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; [email protected] (S.H.); [email protected] (A.K.) 5 Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7 A, FI-90014 Oulu, Finland; andre.juffer@oulu.fi 6 School of Pharmacy, University of Eastern Finland, FI-70210 Kuopio, Finland; maija.lahtela-kakkonen@uef.fi (M.L.-K.); tatu.pantsar@uef.fi -
Is an Activator of the Human Estrogen Receptor Alpha
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Newcastle University E-Prints 1 The ionic liquid 1-octyl-3-methylimidazolium (M8OI) is an activator of the human estrogen receptor alpha Alistair C. Leitch1, Anne F. Lakey1, William E. Hotham1, Loranne Agius1, George E.N. Kass2, Peter G. Blain1, Matthew C. Wright1,* 1Institute Cellular Medicine, Health Protection Research Unit, Level 4 Leech, Newcastle University, Newcastle Upon Tyne, United Kingdom NE24HH. 2European Food Safety Authority, Via Carlo Magno 1A, 43126 Parma, Italy. *Corresponding author. Address: Institute Cellular Medicine, Level 4 Leech Building; Newcastle University, Framlington Place, Newcastle Upon Tyne, UK. [email protected] Email addresses: [email protected] (A. Leitch), [email protected] (A. Lakey), [email protected] (W. Hotham), [email protected] (L Aguis), , [email protected] (G Kass), [email protected] (P. Blain) [email protected] (M. Wright). Abbreviations AhR, aryl hydrocarbon receptor; ICI182780, also known as fulvestrant; E2, 17β estradiol; EE, ethinylestradiol; ERα, estrogen receptor alpha, also known as NR3A1; ERβ, estrogen receptor beta, also known as ER3A2; M8OI, 1-octyl-3-methylimidazolium chloride, also known as C8min; PBC, primary biliary cholangitis; PPARα, peroxisome proliferator activated receptor alpha; TFF1, trefoil factor 1. 2 ABSTRACT Recent environmental sampling around a landfill site in the UK demonstrated that unidentified xenoestrogens were present at higher levels than control sites; that these xenoestrogens were capable of super-activating (resisting ligand-dependent antagonism) the murine variant 2 ERβ and that the ionic liquid 1-octyl-3-methylimidazolium chloride (M8OI) was present in some samples. -
Memorandum Date: June 6, 2014
DEPARTMENT OF HEALTH & HUMAN SERVICES Public Health Service Food and Drug Administration Memorandum Date: June 6, 2014 From: Bisphenol A (BPA) Joint Emerging Science Working Group Smita Baid Abraham, M.D. ∂, M. M. Cecilia Aguila, D.V.M. ⌂, Steven Anderson, Ph.D., M.P.P.€* , Jason Aungst, Ph.D.£*, John Bowyer, Ph.D. ∞, Ronald P Brown, M.S., D.A.B.T.¥, Karim A. Calis, Pharm.D., M.P.H. ∂, Luísa Camacho, Ph.D. ∞, Jamie Carpenter, Ph.D.¥, William H. Chong, M.D. ∂, Chrissy J Cochran, Ph.D.¥, Barry Delclos, Ph.D.∞, Daniel Doerge, Ph.D.∞, Dongyi (Tony) Du, M.D., Ph.D. ¥, Sherry Ferguson, Ph.D.∞, Jeffrey Fisher, Ph.D.∞, Suzanne Fitzpatrick, Ph.D. D.A.B.T. £, Qian Graves, Ph.D.£, Yan Gu, Ph.D.£, Ji Guo, Ph.D.¥, Deborah Hansen, Ph.D. ∞, Laura Hungerford, D.V.M., Ph.D.⌂, Nathan S Ivey, Ph.D. ¥, Abigail C Jacobs, Ph.D.∂, Elizabeth Katz, Ph.D. ¥, Hyon Kwon, Pharm.D. ∂, Ifthekar Mahmood, Ph.D. ∂, Leslie McKinney, Ph.D.∂, Robert Mitkus, Ph.D., D.A.B.T.€, Gregory Noonan, Ph.D. £, Allison O’Neill, M.A. ¥, Penelope Rice, Ph.D., D.A.B.T. £, Mary Shackelford, Ph.D. £, Evi Struble, Ph.D.€, Yelizaveta Torosyan, Ph.D. ¥, Beverly Wolpert, Ph.D.£, Hong Yang, Ph.D.€, Lisa B Yanoff, M.D.∂ *Co-Chair, € Center for Biologics Evaluation & Research, £ Center for Food Safety and Applied Nutrition, ∂ Center for Drug Evaluation and Research, ¥ Center for Devices and Radiological Health, ∞ National Center for Toxicological Research, ⌂ Center for Veterinary Medicine Subject: 2014 Updated Review of Literature and Data on Bisphenol A (CAS RN 80-05-7) To: FDA Chemical and Environmental Science Council (CESC) Office of the Commissioner Attn: Stephen M. -
Evaluation of Protein-Ligand Docking Methods on Peptide-Ligand
bioRxiv preprint doi: https://doi.org/10.1101/212514; this version posted November 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Evaluation of protein-ligand docking methods on peptide-ligand complexes for docking small ligands to peptides Sandeep Singh1#, Hemant Kumar Srivastava1#, Gaurav Kishor1#, Harinder Singh1, Piyush Agrawal1 and G.P.S. Raghava1,2* 1CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India. 2Indraprastha Institute of Information Technology, Okhla Phase III, Delhi India #Authors Contributed Equally Emails of Authors: SS: [email protected] HKS: [email protected] GK: [email protected] HS: [email protected] PA: [email protected] * Corresponding author Professor of Center for Computation Biology, Indraprastha Institute of Information Technology (IIIT Delhi), Okhla Phase III, New Delhi-110020, India Phone: +91-172-26907444 Fax: +91-172-26907410 E-mail: [email protected] Running Title: Benchmarking of docking methods 1 bioRxiv preprint doi: https://doi.org/10.1101/212514; this version posted November 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT In the past, many benchmarking studies have been performed on protein-protein and protein-ligand docking however there is no study on peptide-ligand docking.