scholarly journals PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation

2018 ◽  
Author(s):  
Moritz Schaefer ◽  
Dr. Djork-Arné Clevert ◽  
Dr. Bertram Weiss ◽  
Dr. Andreas Steffen
Keyword(s):  
Gene Editing ◽  
State Of The Art ◽  
Protein Structures ◽  
Design Tool ◽  
Protein Crystal ◽  
Functional Domain ◽  
Web Based ◽  
Domain Annotation ◽  
Sgrna Design ◽  
Processing Steps

AbstractSummary: sgRNAs targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state-of-the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports HDR template generation for gene editing experiments and the visualization of the mutated amino acids in 3D.Availability and Implementation: PAVOOC is available under https://pavooc.me and accessible using current browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend is implemented in Python 3 and ReactJS respectively. All components run in a simple Docker environment.Contact: [email protected]

scholarly journals PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations

2018 ◽  
Vol 35 (13) ◽  
pp. 2309-2310 ◽  
Author(s):  
Moritz Schaefer ◽  
Djork-Arné Clevert ◽  
Bertram Weiss ◽  
Andreas Steffen
Keyword(s):  
Protein Structures ◽  
Design Tool ◽  
Protein Crystal ◽  
Supplementary Information ◽  
Functional Domain ◽  
Web Based ◽  
Homology Directed Repair ◽  
Guide Rnas ◽  
Sgrna Design ◽  
Repair Template

Abstract Summary Single-guide RNAs (sgRNAs) targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state of the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports homology-directed repair template generation for genome editing experiments and the visualization of the mutated amino acids in 3D. Availability and implementation PAVOOC is available under https://pavooc.me and accessible using modern browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend are implemented in Python 3 and ReactJS, respectively. All components run in a simple Docker environment. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Social and Solidarity Economy Web Information Systems

2014 ◽  
Vol 12 (1) ◽  
pp. 35-52 ◽  
Author(s):  
Mariana Curado Malta ◽  
Ana Alice Baptista ◽  
Cristina Parente
Keyword(s):  
Information Systems ◽  
State Of The Art ◽  
Bibliographic Databases ◽  
Sources Of Information ◽  
Solidarity Economy ◽  
Web Based ◽  
Web Information ◽  
The Social ◽  
Application Profile ◽  
Made In

This paper presents the state of the art on interoperability developments for the social and solidarity economy (SSE) community web based information systems (WIS); it also presents a framework of interoperability for the SSE' WIS and the developments made in a research-in-progress PhD project in the last 3 years. A search on the bibliographic databases showed that so far there are no papers on interoperability initiatives on the SSE, so it was necessary to have other sources of information: a preliminary analysis of the WIS that support SSE activities; and interviews with the representatives of some of the world's most important SSE organisations. The study showed that the WIS are still not interoperable yet. In order to become interoperable a group of the SSE community has been developing a Dublin Corre Application Profile to be used by the SSE community as reference and binding to describe their resources. This paper also describes this on-going process.

scholarly journals Protein crystal lattices are dynamic assemblies: the role of conformational entropy in the protein condensed phase

IUCrJ ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. 130-140 ◽  
Author(s):  
Margarita Dimova ◽  
Yancho D. Devedjiev
Keyword(s):  
Condensed Phase ◽  
Protein Structures ◽  
Van Der Waals Interactions ◽  
Protein Crystal ◽  
Crystal Formation ◽  
Conformational Entropy ◽  
Crystal Lattices ◽  
Crystal Contacts ◽  
First Time

Until recently, the occurrence of conformational entropy in protein crystal contacts was considered to be a very unlikely event. A study based on the most accurately refined protein structures demonstrated that side-chain conformational entropy and static disorder might be common in protein crystal lattices. The present investigation uses structures refined using ensemble refinement to show that although paradoxical, conformational entropy is likely to be the major factor in the emergence and integrity of the protein condensed phase. This study reveals that the role of shape entropy and local entropic forces expands beyond the onset of crystallization. For the first time, the complete pattern of intermolecular interactions by protein atoms in crystal lattices is presented, which shows that van der Waals interactions dominate in crystal formation.

scholarly journals The Narrative Event Diagram

2009 ◽  
pp. 101-118
Author(s):  
Helyn Gould ◽  
Michael Hughes ◽  
Paul Maharg ◽  
Emma Nicol
Keyword(s):  
Professional Learning ◽  
Information Science ◽  
Further Education ◽  
Design Tool ◽  
Design History ◽  
Game Based Learning ◽  
Web Based ◽  
Design Iteration ◽  
The United Kingdom ◽  
Narrative Event

Game-based learning and simulation is a powerful mode of learning, used by industries as diverse as aviation and health sciences. While there are many generic Virtual Learning Environments available to further education and higher education in the United Kingdom, there is no widely available open-source Web-based simulation environment for professional learning. The SIMPLE (SIMulated Professional Learning Environment) project has designed, created, implemented and is in the process of evaluating such an environment in a range of disciplinary settings. The simulations that are being created place both undergraduates and postgraduates in a professional context where their work is, as it will be in the workplace, distributed between tools, colleagues, resources, anticipated, and unanticipated problems. One of the key tools that staff will use to create simulations is the “narrative event diagram”, a design tool as well as a means by which the narrative of the simulation is constructed. This chapter will describe the tool, its design history and context, its current use, and next design iteration. In particular it will show the interdisciplinary genesis of the tool’s design, arising from the confluence of computer science, information science, and narrative theory, and its power in designing professional educational simulations.

Nucleation of protein crystals – a nanoscopic perspective

Nanoscale ◽  
2018 ◽  
Vol 10 (26) ◽  
pp. 12256-12267 ◽  
Author(s):  
Mike Sleutel ◽  
Alexander E. S. Van Driessche
Keyword(s):  
State Of The Art ◽  
Crystal Nucleation ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Historical Overview ◽  
Art Analysis

A historical overview and state-of-the-art analysis of the mechanism of protein crystal nucleation from an experimentalist's perspective.

Web-Based Cad Tools for a Networked Manufacturing Service

1998 ◽  
Author(s):  
Fu-Chung F. Wang ◽  
Paul K. Wright
Keyword(s):  
New Product Development ◽  
Design Tool ◽  
Internet Technology ◽  
Machining Process ◽  
Global Network ◽  
The Internet ◽  
Distributed Design ◽  
Cad Tools ◽  
Web Based ◽  
Design And Manufacturing

Abstract New techniques in Information Technology are now changing not only our daily life, but also the professional practice of product design and manufacturing for new product development. Internet technology in particular opens up another domain for building future CAD/CAM environments. This environment will be a global, network-centric environment with various members providing different software tools, manufacturing facilities, and analysis services for distributed design and fabrication. In this paper, we first briefly describe a vision and current development in a distributed design and manufacturing environment. The paper then emphasizes how current CAD tools will evolve to facilitate the distributed design and fabrication process. In particular, the development of a set of Web-based design tools for fabricating parts using a machining process via the Internet is presented. Experiments on machining 2-1/2 D and freeform parts through this Java-based design tool have shown the feasibility for a networked machining service via the Internet.

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

2019 ◽  
Vol 52 (6) ◽  
pp. 1422-1426
Author(s):  
Rajendran Santhosh ◽  
Namrata Bankoti ◽  
Adgonda Malgonnavar Padmashri ◽  
Daliah Michael ◽  
Jeyaraman Jeyakanthan ◽  
...  
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Data Bank ◽  
Protein Crystal ◽  
Dimensional Structure ◽  
Protein Structure Analysis ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Polypeptide Chains

Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three-dimensional structure was solved using X-ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non-homologous protein structures (25 and 90%). A user-friendly graphical interface with various options has been incorporated, with a provision to view the three-dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.

scholarly journals AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins

2020 ◽  
Vol 49 (D1) ◽  
pp. D630-D638
Author(s):  
Jiawei Wang ◽  
Wei Dai ◽  
Jiahui Li ◽  
Qi Li ◽  
Ruopeng Xie ◽  
...  
Keyword(s):  
Paradigm Shift ◽  
Gene Editing ◽  
Phage Therapy ◽  
State Of The Art ◽  
Sequence Data ◽  
Diverse Range ◽  
Adaptive Immune ◽  
Depth Analysis ◽  
Domains Of Life ◽  
Adaptive Immune Systems

Abstract Anti-CRISPR (Acr) proteins naturally inhibit CRISPR-Cas adaptive immune systems across bacterial and archaeal domains of life. This emerging field has caused a paradigm shift in the way we think about the CRISPR-Cas system, and promises a number of useful applications from gene editing to phage therapy. As the number of verified and predicted Acrs rapidly expands, few online resources have been developed to deal with this wealth of information. To overcome this shortcoming, we developed AcrHub, an integrative database to provide an all-in-one solution for investigating, predicting and mapping Acr proteins. AcrHub catalogs 339 non-redundant experimentally validated Acrs and over 70 000 predicted Acrs extracted from genome sequence data from a diverse range of prokaryotic organisms and their viruses. It integrates state-of-the-art predictors to predict potential Acrs, and incorporates three analytical modules: similarity analysis, phylogenetic analysis and homology network analysis, to analyze their relationships with known Acrs. By interconnecting all modules as a platform, AcrHub presents enriched and in-depth analysis of known and potential Acrs and therefore provides new and exciting insights into the future of Acr discovery and validation. AcrHub is freely available at http://pacrispr.erc.monash.edu/AcrHub/.

scholarly journals Nanomedicines to Deliver mRNA: State of the Art and Future Perspectives

Nanomaterials ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 364 ◽  
Author(s):  
Itziar Gómez-Aguado ◽  
Julen Rodríguez-Castejón ◽  
Mónica Vicente-Pascual ◽  
Alicia Rodríguez-Gascón ◽  
María Ángeles Solinís ◽  
...  
Keyword(s):  
Immune Responses ◽  
Plasmid Dna ◽  
Messenger Rna ◽  
Insertional Mutagenesis ◽  
Gene Editing ◽  
State Of The Art ◽  
Translational Efficiency ◽  
Future Perspectives ◽  
Therapeutic Tool

The use of messenger RNA (mRNA) in gene therapy is increasing in recent years, due to its unique features compared to plasmid DNA: Transient expression, no need to enter into the nucleus and no risk of insertional mutagenesis. Nevertheless, the clinical application of mRNA as a therapeutic tool is limited by its instability and ability to activate immune responses; hence, mRNA chemical modifications together with the design of suitable vehicles result essential. This manuscript includes a revision of the strategies employed to enhance in vitro transcribed (IVT) mRNA functionality and efficacy, including the optimization of its stability and translational efficiency, as well as the regulation of its immunostimulatory properties. An overview of the nanosystems designed to protect the mRNA and to overcome the intra and extracellular barriers for successful delivery is also included. Finally, the present and future applications of mRNA nanomedicines for immunization against infectious diseases and cancer, protein replacement, gene editing, and regenerative medicine are highlighted.

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