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Tools for integrated sequence-structure analysis with UCSF Chimera

Elaine C Meng, Eric F Pettersen, Gregory S Couch, Conrad C Huang, Thomas E Ferrin
2006 BMC Bioinformatics  
We describe enhancements to UCSF Chimera to achieve these goals. The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures.  ...  While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where  ...  Morris for comments on this manuscript. UCSF Chimera development is funded by the NIH National Center for Research Resources (grant P41-RR01081).  ... 
doi:10.1186/1471-2105-7-339 pmid:16836757 pmcid:PMC1570152 fatcat:dbl2rom22ng6hidcrx5cjfukhu

Integrative visual analysis of protein sequence mutations

Nadezhda T Doncheva, Karsten Klein, John H Morris, Michael Wybrow, Francisco S Domingues, Mario Albrecht
2014 BMC Proceedings  
Here, we present a novel visual approach for analyzing residue mutations. It combines different biological visualizations and integrates them with molecular data derived from external resources.  ...  Our visual approach and software greatly facilitate the integrative and interactive analysis of protein mutations based on complementary visualizations.  ...  The UCSF Chimera sequence tool was used to view, align and explore the parent and defective TIM sequences.  ... 
doi:10.1186/1753-6561-8-s2-s2 pmid:25237389 pmcid:PMC4155609 fatcat:wlya7upofrf7vay3pfbpqj2x3y

Enhancing UCSF Chimera through web services

Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin
2014 Nucleic Acids Research  
We describe how we have enhanced UCSF Chimera (, a program for the interactive visualization and analysis of molecular structures and related data, through the addition  ...  We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example  ...  In particular, we note the excellent support we received from Luca Clementi who helped us get Opal 2.5 running with Tomcat 6 in our environment.  ... 
doi:10.1093/nar/gku377 pmid:24861624 pmcid:PMC4086125 fatcat:jqsigsatobbvrepwsreuwnv6kq

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps

J. E. Chen, C. C. Huang, T. E. Ferrin
2014 Bioinformatics  
We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts.  ...  We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts.  ...  ACKNOWLEDGEMENT We thank Elaine Meng for careful proofreading of the manuscript. Funding: This work was supported by NIH grant NIGMS P41-GM103311 and the UCSF-Lowell Summer Internship Program.  ... 
doi:10.1093/bioinformatics/btu841 pmid:25540183 pmcid:PMC4410660 fatcat:aaofce2cfzfojgv5ht6skaf5iy

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

Zheng Yang, Keren Lasker, Dina Schneidman-Duhovny, Ben Webb, Conrad C. Huang, Eric F. Pettersen, Thomas D. Goddard, Elaine C. Meng, Andrej Sali, Thomas E. Ferrin
2012 Journal of Structural Biology  
Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera.  ...  X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera  ...  Steven Ludtke for providing the SAXS experimental data for the GroEL example. The research of K. Lasker was supported by continuous mentorship from Prof. Haim J.  ... 
doi:10.1016/j.jsb.2011.09.006 pmid:21963794 pmcid:PMC3410985 fatcat:euxgqtlkzvcbvgswfvzulfuo7y

Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

Sania Safdar Butt, Yasmin Badshah, Maria Shabbir, Mehak Rafiq
2020 JMIR Bioinformatics and Biotechnology  
To date, many software and tools for docking have been employed.  ...  Experimental strategies are integrated with computational approaches for the identification, characterization, and development of novel drugs and compounds.  ...  Use of UCSF Chimera for Docking the Target Protein UCSF Chimera is an extensible program that is meant mainly for visualization and analysis of the molecular structures.  ... 
doi:10.2196/14232 fatcat:pcdnvelqlfao7iokl2bgoyyuve

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures

Jan Kosinski, Alexander von Appen, Alessandro Ori, Kai Karius, Christoph W. Müller, Martin Beck
2015 Journal of Structural Biology  
Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM  ...  To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures  ...  Rashid for providing purified Pol I sample for XL-MS analysis, Luis Pedro Coelho for advice on machine learning, Thomas Bock, Svetlana Dodonova, Niklas Hoffmann, and Noella Silva Martin from EMBL Structural  ... 
doi:10.1016/j.jsb.2015.01.014 pmid:25661704 pmcid:PMC4359615 fatcat:adfvzhu52ngczi3ki3nhwrcxsa

In silico analysis of CDC73 gene revealing 11 novel SNPs with possible association to Hyperparathyroidism-Jaw Tumor syndrome

Abdelrahman H. Abdelmoneim, Alaa I. Mohammed, Esraa O. Gadim, Mayada Alhibir Mohammed, Sara H. Hamza, Sara A. Mirghani, Thwayba A. Mahmoud, Mohamed A. Hassan
2020 The EuroBiotech Journal  
Method: Computational analysis using twelve different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, P-Mut, I-Mutant ,Project Hope, Chimera, COSMIC and dbSNP Short Genetic  ...  The aim of this study is to assess the most deleterious SNPs mutations on CDC73 gene and to predict their influence on the functional and structural levels using different bioinformatics tools.  ...  Chimera software was used to show the 3D changes in the structure of the protein coupled with 2D schematic structures from project hope for comparison ( Fig. 2-12) .  ... 
doi:10.2478/ebtj-2020-0008 fatcat:rjvzwnmouvhxzeboo4k2pgve44

Molecular Structure Properties of Heme Group in the Oxymyoglobin Protein (1mbo.pdb) Using PyMOL & UCSF Chimera

Chetanath Neupane, Seeram Ramakrishna, Jeevan Jyoti Nakarmi, Binod Adhikari
2020 Nanoarchitectonics  
PyMOL and UCSF Chimera are open source multifunctional molecular visualization system developed for the use in structural biology.  ...  Implementing structural analysis feature of UCSF Chimera, the distance between iron core of heme group and molecular oxygen and that between iron core and histidine 93(H93) have been estimated and found  ...  It is now started to integrate MODELLER (it is used for homology or comparative modelling of three dimensional structures) and other modeling tools for structural modeling of multiprotein complexes from  ... 
doi:10.37256/nat.122020425 fatcat:edd77uayljar3f5yoer4hbpu4q

Identification of similar regions of protein structures using integrated sequence and structure analysis tools

Brandon Peters, Charles Moad, Eunseog Youn, Kris Buffington, Randy Heiland, Sean Mooney
2006 BMC Structural Biology  
environments that make that match using a suite of sequence and structure analysis tools.  ...  We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools.  ...  Acknowledgements We would like to thank Giselle Knudsen for helpful comments.  ... 
doi:10.1186/1472-6807-6-4 pmid:16526955 pmcid:PMC1435900 fatcat:pjjbmcg5gfcclgcpwuyqb234hy

UCSF Chimera?A visualization system for exploratory research and analysis

Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin
2004 Journal of Computational Chemistry  
Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics  ...  trajectories; and Volume Viewer, for display and analysis of volumetric data.  ...  Acknowledgments We thank David Konerding and Joe Murray for their contributions to early versions of Chimera. We would also like to thank Patricia  ... 
doi:10.1002/jcc.20084 pmid:15264254 fatcat:f7kzbqy7cve5rg7wmzoty2xoty

Computational vaccinology approach: Designing an efficient multi-epitope peptide vaccine against Cryptococcus neoformans var. grubii heat shock 70KDa protein [article]

Reham Mirghani Elhassan, Nagla Mohammed Alsony, Khadeejah Mohammed Othman, Duaa Tariq Izz-Aldin, Tamadour Abualkhair Alhaj, Abdelrahman Abualgasim Ali, Lena Abdelwahab Abashir, Omar Hashim Ahmed, Mohammed Ahmed Hassan
2019 bioRxiv   pre-print
Then the proposed epitopes were subjected to Population coverage analysis tool to compute the global population coverage.  ...  Therefore, there is a definite need for experimental validation for the carefully chosen vaccine candidates in vitro and in vivo to fortify their antigenic and immunogenic potentials.  ...  Figure 8 . 8 Figure 8.Structural location of YVYDTRGKL as a promising MHC-I binder, with massive population coverage, within the 3D structure of C. neoformans's heat shock 70KDa protein using UCSF chimera  ... 
doi:10.1101/534008 fatcat:6nvaoqj3vvejlb24iu3dcp547u

Integrated Tools for Structural and Sequence Alignment and Analysis

Conrad C. Huang, Walter R. Novak, Patricia C. Babbitt, Andrew I. Jewett, Thomas E. Ferrin, Teri E. Klein
1999 Biocomputing 2000  
These methods ( MinRMS , AlignPlot and MSFviewer ) integrate sequence and structural information and are implemented as separate but cooperating programs to our Chimera molecular modeling system.  ...  Integration of multiple sequence alignment information and three-dimensional structural representations enable researchers to generate hypotheses about the sequence-structure relationship.  ...  Acknowledgments This work is supported by the Department of Energy (DE-FG03-96ER62269), NIH National Center for Research Resources (P41-RR01081) and NIH (AR17323).  ... 
doi:10.1142/9789814447331_0022 fatcat:2rlreqgghjhqhgvk67mfxtszvu

Evaluation of cancer related missense mutations in CENPH

2019 Acta Medica  
The protein structure of the CENPH protein was generated with I-TASSER and missense mutations were visualized on CENPH protein with UCSF Chimera.  ...  Structural effects of selected mutations were assessed with HOPE. Results: 34 missense mutations were observed in human cancers.  ...  As a result, the PredictSNP prediction and predictions of each integrated tool were reported for missense mutations as neutral or deleterious along with expected accuracies.  ... 
doi:10.32552/2019.actamedica.385 fatcat:ophlggxjhffsxdujpyhshfvioi
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