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arXiv 2023年

作者： Lubiana, Tiago Lopes, Rafael Medeiros, Pedro Silva, Juan Carlo Goncalves, Andre Nicolau Aquime Maracaja-Coutinho, Vinicius Nakaya, Helder I. School of Pharmaceutical Sciences University of São Paulo São Paulo Brazil Department of Epidemiology of Microbial Diseases Public Health Modeling Unit Yale School of Public Health New HavenCT United States TauGC Bioinformatics São Paulo Brazil Oxford Vaccine Group University of Oxford Oxford United Kingdom Advanced Center for Chronic Diseases Universidad de Chile Santiago Chile Centro de Modelamiento Molecular Biofísica y Bioinformática - CM2B2 Facultad de Ciencias Químicas y Farmacéuticas Universidad de Chile Santiago Chile ANID Anillo ACT210004 SYSTEMIX Rancagua Chile Anillo Inflammation in HIV/AIDS - InflammAIDS Santiago Chile Beagle Bioinformatics Brasil & Santiago São Paulo Brazil Hospital Israelita Albert Einstein São Paulo Brazil

The rise of advanced chatbots, such as ChatGPT, has sparked curiosity in the scientific community. ChatGPT is a general-purpose chatbot powered by large language models (LLMs) GPT-3.5 and GPT-4, with the potential to impact numerous fields, including computational biology. In this article, we offer ten tips based on our experience with ChatGPT to assist computational biologists in optimizing their workflows. We have collected relevant prompts and reviewed the nascent literature in the field, compiling tips we project to remain pertinent for future ChatGPT and LLM iterations, ranging from code refactoring to scientific writing to prompt engineering. We hope our work will help bioinformaticians to complement their workflows while staying aware of the various implications of using this technology. Additionally, to track new and creative applications for bioinformatics tools such as ChatGPT, we have established a GitHub repository at https://***/csbl-br/awesome-compbio-chatgpt. Our belief is that ethical adherence to ChatGPT and other LLMs will increase the efficiency of computational biologists, ultimately advancing the pace of scientific discovery in the life *** Codes 92-04 © 2023, CC BY-SA.

关键词： Computational efficiency

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Deciphering the therapeutic role of Kigelia africana fruit in erectile dysfunction through metabolite profiling and molecular modelling

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Informatics in Medicine Unlocked 2023年 37卷

作者： Olawale, Femi Olofinsan, Kolawole Ogunyemi, Oludare M. Karigidi, Kayode O. Gyebi, Gideon A. Ibrahim, Ibrahim M. Iwaloye, Opeyemi Department of Biochemistry University of Lagos Nigeria Department of Biochemistry University of KwaZulu South Africa Department of Biochemistry Nile University of Nigeria Nigeria Computational Biology and Biomolecular Modeling Laboratories Department of Biochemistry School of Basic Medical Sciences Babcock University Ogun State Illishan-Remo Nigeria Department of Biochemistry Olusegun Agagu University of Science and Technology Okitipupa Nigeria Department of Biochemistry Faculty of Science and Technology Bingham University Nasarawa Karu Nigeria Department of Biophysics Faculty of Sciences Cairo University Giza Egypt Bioinformatics and Molecular Biology Unit Department of Biochemistry Federal University of Technology Akure P.M.B. 704 Ondo State Akure 360001 Nigeria

Kigelia africana herbal products are often used traditionally to treat erectile dysfunction and other sexual complaints, but the underlying mechanism is not yet understood. This study focused on profiling the bioactive constituents of Kigelia africana fruit (KAF) using spectroscopic techniques and providing the computational models of their interactions with phosphodiesterase (PDE5) and Rho-associated coiled-coil containing protein kinase 2 (ROCK2) targets associated with erectile dysfunction. Integrated FT-IR, HPLC-MS, and GC-MS analysis revealed 152 (C1–C152) KAF compounds with highly diverse functional groups and chemical properties. molecular docking showed several hit compounds as potential inhibitors of PDE5 and ROCK2. Post docking MMGBSA, QSAR, predictive physicochemical analysis and AdmetSAR analysis revealed that most of the hit compounds are potential drug leads. Among these, hydroxydoxepin (C3) and ritodrine (C131) exhibited the strongest interactions with PDE5, while epigallocatechin 3-O-p-coumarate (C9) and chlorogenic acid (C91) had the strongest interaction with ROCK2. The thermodynamic parameters and trajectory clusters computed from the trajectories obtained from the 100 ns full atomistic molecular dynamic (MD) simulation indicated the structural stability and conformational flexibility of the selected complexes. The MD simulation-based MMPBSA calculation further revealed strong binding affinity and energy contribution by active site residues of PDE5 towards binding the selected KAF compounds. Various computational analyses employed revealed that the catalytic residues Gln817, Val782 and Phe786 of PDE5 exhibited high interaction potential and flexibility towards C3 and C131. Overall, hydroxydoxepin, ritodrine and other phytochemicals in Kigelia africana may account for the therapeutic role of this plant in erectile dysfunction. © 2023

关键词： Erectile dysfunction Kigelia africana molecular docking and dynamics Phytochemical analysis QSAR

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Isoleucine gate blocks K+ conduction in C-type inactivation

arXiv

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arXiv 2024年

作者： Treptow, Werner Liu, Yichen Bassetto, Carlos A.Z. Pinto, Bernardo I. Alves, João Chipot, Christophe Bezanilla, Francisco Roux, Benoît Universidade de Brasília DF CEP 70904-970 Brazil Department of Biochemistry and Molecular Biology The University of Chicago ChicagoIL60637 United States Department of Neurobiology The University of Chicago ChicagoIL60637 United States Laboratoire International Associe Centre National de la Recherche Scientifique University of Illinois at Urbana−Champaign Université de Lorraine Université de Lorraine Unité Mixte de Recherche No. 7019 B.P. 70239 Vandœuvre-lès-Nancy cedex 54506 France NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology Department of Physics University of Illinois at Urbana−Champaign UrbanaIL61801 United States Centro Interdisciplinario de Neurociencia de Valparaíso Facultad de Ciencias Universidad de Valparaíso Valparaíso Chile

Many voltage-gated potassium (Kv) channels display a time-dependent phenomenon called C-type inactivation, whereby prolonged activation by voltage leads to the inhibition of ionic conduction, a process that involves a conformational change at the selectivity filter toward a non-conductive state. Recently, a high-resolution structure of a strongly inactivating triple-mutant channel kv1.2-kv2.1-3m revealed a novel conformation of the selectivity filter that is dilated at its outer end, distinct from the well-characterized conductive state. While the experimental structure was interpreted as the elusive non-conductive state, molecular dynamics simulations and electrophysiology measurements demonstrate that the dilated filter of kv1.2-kv2.1-3m, however, is conductive and, as such, cannot completely account for the inactivation of the channel observed in functional experiments. An additional conformational change implicating isoleucine residues at position 398 along the pore lining segment S6 is required to effectively block ion conduction. It is shown that the I398 residues from the four subunits act as a state-dependent hydrophobic gate located immediately beneath the selectivity filter. As a critical piece of the C-type inactivation machinery, this structural feature is the potential target of a broad class of QA blockers and negatively charged activators thus opening new research directions towards the development of drugs that specifically modulate gating-states of Kv channels. © 2024, CC BY.

关键词： Electrophysiology

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Engineered CD4 TCR T cells with conserved high-affinity TCRs targeting NY-ESO-1 for advanced cellular therapies in cancer

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Science Advances 2025年第26期11卷

作者： Margaux Saillard Mara Cenerenti Patrick Reichenbach Philippe Guillaume Ziyang Su Morteza Hafezi Julien Schmidt Julien Cesbron Raphaël Genolet Lise Queiroz Julien Racle Jean Villard Raffaele Renella Olivier Michielin Vincent Zoete Jean-Paul Rivals Melita Irving Daniel E. Speiser Alexandre Harari David Gfeller Olivier Adotevi Francesco Ceppi George Coukos Pedro Romero Camilla Jandus Department of Oncology UNIL CHUV University of Lausanne Lausanne Switzerland. Ludwig Institute for Cancer Research Lausanne Switzerland. Department of Pathology and Immunology University of Geneva Geneva Switzerland. Translational Research Centre in Onco-Hematology (CRTOH) University of Geneva Geneva Switzerland. Geneva Centre for Inflammation Research (GCIR) University of Geneva Geneva Switzerland. SIB Swiss Institute of Bioinformatics Lausanne Switzerland. Division of Nephrology Geneva University Hospitals Geneva Switzerland. Division of Transplantation Immunology Geneva University Hospitals Geneva Switzerland. Pediatric Hematology-Oncology Unit Division of Pediatrics Department “Woman-Mother-Child” University Hospital and Lausanne University Lausanne Switzerland. Molecular Modeling Group SIB Swiss Institute of Bioinformatics Lausanne Switzerland. Department of Oncology Geneva University Hospitals Geneva Switzerland. Plateforme clinique et translationnelle Centre des thérapies expérimentales University Hospital and Lausanne University Lausanne Switzerland. Université Bourgogne Franche-Comté INSERM EFS BFC UMR1098 Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique Besançon France.

While cancer immunotherapy has primarily focused on CD8 T cells, CD4 T cells are increasingly recognized for their role in antitumor immunity. The HLA-DRB3*02:02 allele is found in 50% of Caucasians. In this study, we screened HLA-DRB3*02:02 patients with melanoma for tumor-specific CD4 T cells and identified robust New York esophageal squamous cell carcinoma 1 (NY-ESO-1)123–137/HLA-DRB3*02:02 CD4 T cell activity in both peripheral blood and tumor tissue. By analyzing NY-ESO-1123–137/HLA-DRB3*02:02–restricted CD4 T cell clones, we uncovered an unexpectedly high cytotoxicity, strong T helper 1 polarization, and recurrent αβ T cell receptor (TCRαβ) usage across patients and anatomical sites. These responses were also present in other NY-ESO-1–expressing cancers. TCRs from these clones, when transduced into primary CD4 T cells, showed direct antitumor efficacy both in vitro and in vivo. Our findings suggest that these TCRs are promising for adoptive T cell transfer therapy, enabling broader targeting of NY-ESO-1–expressing adult and pediatric cancers in clinical settings.

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PLUMED Tutorials: a collaborative, community-driven learning ecosystem

arXiv

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arXiv 2024年

作者： Tribello, Gareth A. Bonomi, Massimiliano Bussi, Giovanni Camilloni, Carlo Armstrong, Blake I. Arsiccio, Andrea Aureli, Simone Ballabio, Federico Bernetti, Mattia Bonati, Luigi Brookes, Samuel G.H. Faidon Brotzakis, Z. Capelli, Riccardo Ceriotti, Michele Chan, Kam-Tung Cossio, Pilar Dasetty, Siva Donadio, Davide Ensing, Bernd Ferguson, Andrew L. Fraux, Guillaume Gale, Julian D. Gervasio, Francesco Luigi Giorgino, Toni Herringer, Nicholas S.M. Hocky, Glen M. Hoff, Samuel E. Invernizzi, Michele Languin-Cattoën, Olivier Leone, Vanessa Limongelli, Vittorio Lopez-Acevedo, Olga Marinelli, Fabrizio Martinez, Pedro Febrer Masetti, Matteo Mehdi, Shams Michaelides, Angelos Murtada, Mhd Hussein Parrinello, Michele Piaggi, Pablo M. Pietropaolo, Adriana Pietrucci, Fabio Pipolo, Silvio Pritchard, Claire Raiteri, Paolo Raniolo, Stefano Rapetti, Daniele Rizzi, Valerio Rydzewski, Jakub Salvalaglio, Matteo Schran, Christoph Seal, Aniruddha Zadeh, Armin Shayesteh Silva, Tomás F.D. Spiwok, Vojtěch Stirnemann, Guillaume Sucerquia, Daniel Tiwary, Pratyush Valsson, Omar Vendruscolo, Michele Voth, Gregory A. White, Andrew D. Wu, Jiangbo Centre for Quantum Materials and Technology School of Mathematics and Physics Queen’s University Belfast United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Via Bonomea 265 Trieste34136 Italy Department of Biosciences University of Milano Milano Italy School of Molecular and Life Sciences Curtin University GPO Box U1987 PerthWA6845 Australia Coriolis Pharma Fraunhoferstrasse 18b Martinsried82152 Germany School of Pharmaceutical Sciences University of Geneva Rue Michel-Servet 1 GenevaCH-1206 Switzerland Institute of Pharmaceutical Sciences of Western Switzerland University of Geneva GenevaCH-1206 Switzerland Swiss Bioinformatics Institute University of Geneva GenevaCH-1206 Switzerland Via Celoria 26 Milan20133 Italy Department of Biomolecular Sciences University of Urbino "Carlo Bo" Piazza Rinascimento 6 Urbino61029 Italy Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna Via Belmeloro 6 Bologna40126 Italy Atomistic Simulations Italian Institute of Technology Genova Italy Yusuf Hamied Department of Chemistry University of Cambridge CambridgeCB2 1EW United Kingdom Institute for Bioinnovation Biomedical Sciences Research Center "Alexander Fleming" Vari16672 Greece Laboratory of Computational Science and Modeling Institut des Matériaux École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Chemistry University of California Davis DavisCA95616 United States Center for Computational Mathematics Flatiron Institute New YorkNY10010 United States Center for Computational Biology Flatiron Institute New YorkNY10010 United States Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States AI4Science Lab Informatics Institute University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Computational Chemistry Group Van’t Hoff Institute for Molecular Sciences Unive

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities. To address these issues, here we introduce "PLUMED Tutorials", a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources. © 2024, CC BY.

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Pressing topics in the Belgian water sector anno 2015

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Sustainability of Water Quality and Ecology 2016年 7卷 32-36页

作者： De Mulder, C. Van Hoey, S. Van Hulle, S. Agathos, S.N. Cauwenberg, P. Mergen, P. Seuntjens, P. Smets, I. De Gueldre, G. Mouton, A. Schowanek, D. Meesschaert, B. Verstraete, W. Nopens, I. BIOMATH Department of Mathematical Modelling Statistics and Bioinformatics Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium LIWET Department of Industrial Biological Sciences Ghent University Graaf Karel de Goedelaan 5 Kortrijk 8500 Belgium Laboratory of Bioengineering Earth and Life Institute Université Catholique de Louvain Louvain-la-Neuve 1348 Belgium Unit Environmental Modeling Flemish Institute for Technological Research (VITO) Boeretang 200 Mol 2400 Belgium Royal Museum for Central Africa Leuvensesteenweg 13 Tervuren 3080 Belgium Botanic Garden Meise Bouchout Domain Nieuwelaan 38 Meise 1860 Belgium Department of Soil Management Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium Department of Bioscience Engineering University of Antwerp Groenenborgerlaan 171 Antwerpen 2000 Belgium CREaS Department of Chemical Engineering KU Leuven Celestijnenlaan 200F Leuven 3001 Belgium Aquafin NV Dijkstraat 8 Aartselaar 2630 Belgium Technology Campus Gent Odisee Hogeschool Gebroeders De Smetstraat 1 Gent 9000 Belgium Environmental Stewardship and Sustainability - Brussels Innovation Center Procter and Gamble Temselaan 100 Strombeek-Bever 1853 Belgium Cluster for Bioengineering Technology Department of Microbial and Molecular Systems KU Leuven Technology Campus Ostend Zeedijk 101 Oostende B-8400 Belgium LabMET Department of Biochemical and Microbial Technology Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent 9000 Belgium

Today's water sector is governed by some hot topics, and this is no different in Belgium. As for the International Water Association (IWA), the goal of its Belgian division (B-IWA) is to gather different stakeholders, i.e. academics, policy makers and people from industry active in the (Belgian) water sector and trigger the debate. In May 2015, a first Nocturnal was organised to accomplish just this. Seven hot water topics, proposed by participants at the time of their online registration, were addressed in rotating round table discussions. These topics included resource recovery, micropollutants, water scarcity, hydroinformatics, integrated water management and modeling, technology vs. legislation and Computational Fluid Dynamics in water applications. The lively discussions led to the idea of this short contribution describing the outcomes of these round table discussions, along with some additional research on the topics. Main conclusions include the need for education (both of scholars and young professionals), inter-domain communication and the growing importance of IT in the water sector. © 2016 Elsevier B.V.

关键词： Education Industry Informatics Legislation Water sector

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Author Correction: Federated learning enables big data for rare cancer boundary detection

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Nature communications 2023年第1期14卷 436页

作者： Sarthak Pati Ujjwal Baid Brandon Edwards Micah Sheller Shih-Han Wang G Anthony Reina Patrick Foley Alexey Gruzdev Deepthi Karkada Christos Davatzikos Chiharu Sako Satyam Ghodasara Michel Bilello Suyash Mohan Philipp Vollmuth Gianluca Brugnara Chandrakanth J Preetha Felix Sahm Klaus Maier-Hein Maximilian Zenk Martin Bendszus Wolfgang Wick Evan Calabrese Jeffrey Rudie Javier Villanueva-Meyer Soonmee Cha Madhura Ingalhalikar Manali Jadhav Umang Pandey Jitender Saini John Garrett Matthew Larson Robert Jeraj Stuart Currie Russell Frood Kavi Fatania Raymond Y Huang Ken Chang Carmen Balaña Jaume Capellades Josep Puig Johannes Trenkler Josef Pichler Georg Necker Andreas Haunschmidt Stephan Meckel Gaurav Shukla Spencer Liem Gregory S Alexander Joseph Lombardo Joshua D Palmer Adam E Flanders Adam P Dicker Haris I Sair Craig K Jones Archana Venkataraman Meirui Jiang Tiffany Y So Cheng Chen Pheng Ann Heng Qi Dou Michal Kozubek Filip Lux Jan Michálek Petr Matula Miloš Keřkovský Tereza Kopřivová Marek Dostál Václav Vybíhal Michael A Vogelbaum J Ross Mitchell Joaquim Farinhas Joseph A Maldjian Chandan Ganesh Bangalore Yogananda Marco C Pinho Divya Reddy James Holcomb Benjamin C Wagner Benjamin M Ellingson Timothy F Cloughesy Catalina Raymond Talia Oughourlian Akifumi Hagiwara Chencai Wang Minh-Son To Sargam Bhardwaj Chee Chong Marc Agzarian Alexandre Xavier Falcão Samuel B Martins Bernardo C A Teixeira Flávia Sprenger David Menotti Diego R Lucio Pamela LaMontagne Daniel Marcus Benedikt Wiestler Florian Kofler Ivan Ezhov Marie Metz Rajan Jain Matthew Lee Yvonne W Lui Richard McKinley Johannes Slotboom Piotr Radojewski Raphael Meier Roland Wiest Derrick Murcia Eric Fu Rourke Haas John Thompson David Ryan Ormond Chaitra Badve Andrew E Sloan Vachan Vadmal Kristin Waite Rivka R Colen Linmin Pei Murat Ak Ashok Srinivasan J Rajiv Bapuraj Arvind Rao Nicholas Wang Ota Yoshiaki Toshio Moritani Sevcan Turk Joonsang Lee Snehal Prabhudesai Fanny Morón Jacob Mandel Konstantinos Kamnitsas Ben Glocker Luke V M Dixon Matthew Williams Peter Zamp Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA. Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Informatics Technical University of Munich Munich Bavaria Germany. Intel Corporation Santa Clara CA USA. Department of Neuroradiology Heidelberg University Hospital Heidelberg Germany. Clinical Cooperation Unit Neuropathology German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Neuropathology Heidelberg University Hospital Heidelberg Germany. Division of Medical Image Computing German Cancer Research Center Heidelberg Germany. Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany. Neurology Clinic Heidelberg University Hospital Heidelberg Germany. Department of Radiology & Biomedical Imaging University of California San Francisco San Francisco CA USA. Symbiosis Center for Medical Image Analysis Symbiosis International University Pune Maharashtra India. Department of Neuroimaging and Interventional Radiology National Institute of Mental Health and Neurosciences Bangalore Karnataka India. Department of Radiology School of Medicine and Public Health University of Wisconsin Madison WI USA. Department of Medical Physics School of Medicine and Public Health University of Wisconsin Madison WI USA. Leeds Teaching Hospitals Trust Department of Radiology Leeds UK. Department of Radiology Brigham and Women's Hospital Harvard Medical School Boston MA USA. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA USA. Catalan Institute of Oncology Badalona Spain. Consorci MAR Parc de Salut de Barcelona Catalonia Spain. Department of Radiology (IDI

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers

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Biophysical Journal 2007年第11期92卷 3817-3829页

作者： Pérez, Alberto Marchán, Iván Svozil, Daniel Sponer, Jiri Cheatham III, Thomas E. Laughton, Charles A. Orozco, Modesto Molecular Modeling and Bioinformatics Unit Institut de Recerca Biomèdica Parc Científic de Barcelona Barcelona 08028 Spain Computational Biology Program Barcelona Supercomputer Centre Edifici Torre Girona Barcelona 08028 Spain Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems Academy of Sciences of the Czech Republic 166 10 Prague 6 Czech Republic Institute of Biophysics Academy of Sciences of the Czech Republic 612 65 Brno Czech Republic Faculty of Science Masaryk University 611 37 Brno Czech Republic Departments of Medicinal Chemistry Pharmaceutical Chemistry and Pharmaceutics and Bioengineering University of Utah Salt Lake City UT 84112 United States School of Pharmacy Centre for Biomolecular Sciences University of Nottingham Nottingham NG7 2RD United Kingdom Departament de Bioquímica I Biología Molecular Facultat de Biología Universitat de Barcelona Barcelona 08028 Spain

We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the α/γ concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the α/γ = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 μs of state-of-the-art molecular dynamics simulations in aqueous solution. © 2007 by the Biophysical Society.

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