1
|
Zhang Y, Yang C, Xiong Y, Xiao Y. 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures. Biophys J 2024; 123:2696-2704. [PMID: 38409781 PMCID: PMC11393702 DOI: 10.1016/j.bpj.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
DNA molecules are vital macromolecules that play a fundamental role in many cellular processes and have broad applications in medicine. For example, DNA aptamers have been rapidly developed for diagnosis, biosensors, and clinical therapy. Recently, we proposed a computational method of predicting DNA 3D structures, called 3dDNA. However, it lacks a scoring function to evaluate the predicted DNA 3D structures, and so they are not ranked for users. Here, we report a scoring function, 3dDNAscoreA, for evaluation of DNA 3D structures based on a deep learning model ARES for RNA 3D structure evaluation but using a new strategy for training. 3dDNAscoreA is benchmarked on two test sets to show its ability to rank DNA 3D structures and select the native and near-native structures.
Collapse
Affiliation(s)
- Yi Zhang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chenxi Yang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiduo Xiong
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| |
Collapse
|
2
|
Zhang Y, Xiong Y, Yang C, Xiao Y. 3dRNA/DNA: 3D Structure Prediction from RNA to DNA. J Mol Biol 2024; 436:168742. [PMID: 39237199 DOI: 10.1016/j.jmb.2024.168742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 07/03/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024]
Abstract
There is an increasing need for determining 3D structures of DNAs, e.g., for increasing the efficiency of DNA aptamer selection. Recently, we have proposed a computational method of 3D structure prediction of DNAs, called 3dDNA, which has been integrated into our original web server 3dRNA, now renamed 3dRNA/DNA (http://biophy.hust.edu.cn/new/3dRNA). Currently, 3dDNA can only output the predicted DNA 3D structures for users but cannot rank them as an energy function for assessing DNA 3D structures is still lacking. Here, we first provide a brief introduction to 3dDNA and then introduce a new energy function, 3dDNAscore, for the assessment of DNA 3D structures. 3dDNAscore is an all-atom knowledge-based potential by integrating 86 atomic types from nucleic acids. Benchmarks demonstrate that 3dDNAscore can effectively identify near-native structures from the decoys generated by 3dDNA, thus enhancing the completeness of 3dDNA.
Collapse
Affiliation(s)
- Yi Zhang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yiduo Xiong
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Chenxi Yang
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
| |
Collapse
|
3
|
Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Int J Mol Sci 2022; 23:ijms23179630. [PMID: 36077037 PMCID: PMC9455975 DOI: 10.3390/ijms23179630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 01/19/2023] Open
Abstract
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.
Collapse
Affiliation(s)
- Julita Gumna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Antczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Ryszard W. Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Jun Li
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Laboratory of Computational Biology, Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | | | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Sicheng Zhang
- Department of Physics, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- Correspondence: (Z.M.); (A.R.)
| | - Marta Szachniuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Agnieszka Rybarczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
- Correspondence: (Z.M.); (A.R.)
| |
Collapse
|
4
|
Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res 2020; 48:576-588. [PMID: 31799609 PMCID: PMC7145511 DOI: 10.1093/nar/gkz1108] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/06/2019] [Accepted: 11/15/2019] [Indexed: 12/12/2022] Open
Abstract
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.
Collapse
Affiliation(s)
- Marcin Magnus
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Maciej Antczak
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Jakub Wiedemann
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Lukasiak
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 12 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Marta Szachniuk
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
5
|
RNApolis: Computational Platform for RNA Structure Analysis. FOUNDATIONS OF COMPUTING AND DECISION SCIENCES 2019. [DOI: 10.2478/fcds-2019-0012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
In the 1970s, computer scientists began to engage in research in the field of structural biology. The first structural databases, as well as models and methods supporting the analysis of biomolecule structures, started to be created. RNA was put at the centre of scientific interest quite late. However, more and more methods dedicated to this molecule are currently being developed. This paper presents RNApolis - a new computing platform, which offers access to seven bioinformatic tools developed to support the RNA structure study. The set of tools include a structural database and systems for predicting, modelling, annotating and evaluating the RNA structure. RNApolis supports research at different structural levels and allows the discovery, establishment, and validation of relationships between the primary, secondary and tertiary structure of RNAs. The platform is freely available at http://rnapolis.pl
Collapse
|
6
|
Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M. RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. BMC Bioinformatics 2018; 19:304. [PMID: 30134831 PMCID: PMC6106928 DOI: 10.1186/s12859-018-2317-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complement them. Recently, researchers' interests have directed towards in silico methods to fit, remodel and refine RNA tertiary structure models. Their power lies in a problem-specific exploration of RNA conformational space and efficient optimization procedures. The aim is to improve the accuracy of models obtained either computationally or experimentally. RESULTS Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/ CONCLUSIONS: RNAfitme has been applied in various RNA 3D remodeling scenarios for several types of input data. Computational experiments proved its efficiency, accuracy, and usefulness in the processing of RNAs of any size. Fidelity of RNAfitme predictions has been thoroughly tested for RNA 3D structures determined experimentally and modeled in silico.
Collapse
Affiliation(s)
- Maciej Antczak
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.,Poznan Supercomputing and Networking Center, Jana Pawla II 10, 61-139, Poznan, Poland
| | - Maciej Osowiecki
- Department of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ryszard W Adamiak
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| |
Collapse
|
7
|
Wiedemann J, Zok T, Milostan M, Szachniuk M. LCS-TA to identify similar fragments in RNA 3D structures. BMC Bioinformatics 2017; 18:456. [PMID: 29058576 PMCID: PMC5651598 DOI: 10.1186/s12859-017-1867-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022] Open
Abstract
Background In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Results Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds’ rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/. Conclusions The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures. Electronic supplementary material The online version of this article (10.1186/s12859-017-1867-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jakub Wiedemann
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.,Poznan Supercomputing and Networking Center, Jana Pawla II 10, 61-139, Poznan, Poland
| | - Maciej Milostan
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.,Poznan Supercomputing and Networking Center, Jana Pawla II 10, 61-139, Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| |
Collapse
|
8
|
Abstract
Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction.
Collapse
Affiliation(s)
- Zhichao Miao
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67000 Strasbourg, France; ,
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67000 Strasbourg, France; ,
| |
Collapse
|
9
|
Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J. RNAssess--a web server for quality assessment of RNA 3D structures. Nucleic Acids Res 2015; 43:W502-6. [PMID: 26068469 PMCID: PMC4489242 DOI: 10.1093/nar/gkv557] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/16/2015] [Indexed: 01/15/2023] Open
Abstract
Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/
Collapse
Affiliation(s)
- Piotr Lukasiak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Antczak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Tomasz Ratajczak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard W Adamiak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
10
|
Purzycka KJ, Popenda M, Szachniuk M, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches. Methods Enzymol 2015; 553:3-34. [PMID: 25726459 DOI: 10.1016/bs.mie.2014.10.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Understanding the numerous functions of RNAs depends critically on the knowledge of their three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of RNA 3D structures have been assessed using X-ray crystallography, NMR spectroscopy, and cryomicroscopy. This has led to a great demand to obtain the RNA 3D structures using prediction methods. The 3D structure prediction, especially of large RNAs, still remains a significant challenge and there is still a great demand for high-resolution structure prediction methods. In this chapter, we describe RNAComposer, a method and server for the automated prediction of RNA 3D structures based on the knowledge of secondary structure. Its applications are supported by other automated servers: RNA FRABASE and RNApdbee, developed to search and analyze secondary and 3D structures. Another method, RNAlyzer, offers new way to analyze and visualize quality of RNA 3D models. Scope and limitations of RNAComposer in application for an automated prediction of riboswitches' 3D structure will be presented and discussed. Analysis of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z) as an example allows for 3D structure prediction of related riboswitches from Clostridium difficile 4, Bacillus halodurans 1, and Thermus aquaticus Y5.1 of yet unknown structures.
Collapse
Affiliation(s)
- K J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - M Popenda
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - M Szachniuk
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - M Antczak
- European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - P Lukasiak
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - J Blazewicz
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - R W Adamiak
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
| |
Collapse
|
11
|
Olechnovič K, Venclovas C. The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes. Nucleic Acids Res 2014; 42:W259-63. [PMID: 24838571 PMCID: PMC4086110 DOI: 10.1093/nar/gku294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score.
Collapse
Affiliation(s)
- Kliment Olechnovič
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania Faculty of Mathematics and Informatics, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania
| | - Ceslovas Venclovas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
| |
Collapse
|
12
|
Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M. RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Res 2014; 42:W368-72. [PMID: 24771339 PMCID: PMC4086112 DOI: 10.1093/nar/gku330] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee-a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.
Collapse
Affiliation(s)
- Maciej Antczak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Piotr Lukasiak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard W Adamiak
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
13
|
Ding Z, German P, Bai S, Reddy AS, Liu XD, Sun M, Zhou L, Chen X, Zhao X, Wu C, Zhang S, Mills GB, Jonasch E. Genetic and pharmacological strategies to refunctionalize the von Hippel Lindau R167Q mutant protein. Cancer Res 2014; 74:3127-36. [PMID: 24755468 DOI: 10.1158/0008-5472.can-13-3213] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aberrant von Hippel Lindau (VHL) protein function is the underlying driver of VHL-related diseases, including both sporadic and inherited clear cell renal cell carcinoma (ccRCC). About one third of VHL mutations are missense point mutations, with R167Q being the most common VHL point mutation in hereditary VHL disease. Although it has been studied extensively, the ability of VHL-R167Q to downregulate hypoxia-inducible factor 2α (HIF2α) is still controversial. In addition, the manner in which the mutation contributes to tumorigenesis is not fully understood. No therapeutic approach is available to target VHL-R167Q and similar missense point mutations. We analyzed VHL-R167Q proteostasis and function at normoxia, at hypoxia with different oxygen pressure, and in a xenograft mouse model. We showed that the protein levels of VHL-R167Q dictate its ability to downregulate HIF2α and suppress tumor growth. Strikingly, the proteasome inhibitors bortezomib and carfilzomib, which are currently in clinical use, stabilize VHL-R167Q and increase its ability to downregulate HIF2α. VHL-R167Q binds elongin C and elongin B with considerably less avidity than wild-type VHL does but retains residual capacity to generate a VHL-elongin C-elongin B complex, downregulate HIF2α, and suppress tumorigenesis, which could be rescued by increase of VHL-R167Q levels. Finally, we used in silico approaches and identified other missense VHL mutants in addition to VHL-R167Q that might be rescued by similar strategies. Thus, our studies revealed detailed information describing how VHL-R167Q contributes to tumorigenesis and identified a potential targeted therapy for ccRCC and other VHL-related disease in patients carrying VHL-R167Q or similar missense mutations.
Collapse
Affiliation(s)
- Zhiyong Ding
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Peter German
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Shanshan Bai
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - A Srinivas Reddy
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Xian-De Liu
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Mianen Sun
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Lijun Zhou
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Xiaohua Chen
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Xiaobei Zhao
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Chengbiao Wu
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Shuxing Zhang
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Gordon B Mills
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| | - Eric Jonasch
- Authors' Affiliations: Departments of Systems Biology, Genitourinary Medical Oncology, and Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, California
| |
Collapse
|
14
|
Olechnovič K, Venclovas C. The use of interatomic contact areas to quantify discrepancies between RNA 3D models and reference structures. Nucleic Acids Res 2014; 42:5407-15. [PMID: 24623815 PMCID: PMC4027170 DOI: 10.1093/nar/gku191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Growing interest in computational prediction of ribonucleic acid (RNA) three-dimensional structure has highlighted the need for reliable and meaningful methods to compare models and experimental structures. We present a structure superposition-free method to quantify both the local and global accuracy of RNA structural models with respect to the reference structure. The method, initially developed for proteins and here extended to RNA, closely reflects physical interactions, has a simple definition, a fixed range of values and no arbitrary parameters. It is based on the correspondence of respective contact areas between nucleotides or their components (base or backbone). The better is the agreement between respective contact areas in a model and the reference structure, the more accurate the model is considered to be. Since RNA bases account for the largest contact areas, we further distinguish stacking and non-stacking contacts. We have extensively tested the contact area-based evaluation method and found it effective in both revealing local discrepancies and ranking models by their overall quality. Compared to other reference-based RNA model evaluation methods, the new method shows a stronger emphasis on stereochemical quality of models. In addition, it takes into account model completeness, enabling a meaningful evaluation of full models and those missing some residues.
Collapse
Affiliation(s)
- Kliment Olechnovič
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania Faculty of Mathematics and Informatics, Vilnius University, Naugarduko 24, Vilnius LT-03225, Lithuania
| | - Ceslovas Venclovas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
| |
Collapse
|
15
|
Wasik S, Jackowiak P, Figlerowicz M, Blazewicz J. Multi-agent model of hepatitis C virus infection. Artif Intell Med 2013; 60:123-31. [PMID: 24309221 DOI: 10.1016/j.artmed.2013.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 10/23/2013] [Accepted: 11/01/2013] [Indexed: 01/04/2023]
Abstract
OBJECTIVES The objective of this study is to design a method for modeling hepatitis C virus (HCV) infection using multi-agent simulation and to verify it in practice. METHODS AND MATERIALS In this paper, first, the modeling of HCV infection using a multi-agent system is compared with the most commonly used model type, which is based on differential equations. Then, the implementation and results of the model using a multi-agent simulation is presented. To find the values of the parameters used in the model, a method using inverted simulation flow and genetic algorithm is proposed. All of the data regarding HCV infection are taken from the paper describing the model based on the differential equation to which the proposed method is compared. RESULTS Important advantages of the proposed method are noted and demonstrated: these include flexibility, clarity, re-usability and the possibility to model more complex dependencies. Then, the simulation framework that uses the proposed approach is successfully implemented in C++ and is verified by comparing it to the approach based on differential equations. The verification proves that an objective function that performs the best is the function that minimizes the maximal differences in the data. Finally, an analysis of one of the already known models is performed, and it is proved that it incorrectly models a decay in the hepatocytes number by 40%. CONCLUSIONS The proposed method has many advantages in comparison to the currently used model types and can be used successfully for analyzing HCV infection. With almost no modifications, it can also be used for other types of viral infections.
Collapse
Affiliation(s)
- Szymon Wasik
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland.
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|