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Tools for integrated sequence-structure analysis with UCSF Chimera
2006
BMC Bioinformatics
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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
structureViz: linking Cytoscape and UCSF Chimera
2007
Bioinformatics
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to open structures in Chimera and align them using Chimera's sequencestructure analysis tools. ...
UCSF Chimera. ...
With structureViz, multiple levels of abstracted biological data are integrated into a single interface for visualization and analysis. ...
doi:10.1093/bioinformatics/btm329
pmid:17623706
fatcat:ltbgn3m6rfgzxlxkwtpsqxmulm
Integrative visual analysis of protein sequence mutations
2014
BMC Proceedings
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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
2014
Nucleic Acids Research
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We describe how we have enhanced UCSF Chimera (http://www.rbvi.ucsf.edu/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
2014
Bioinformatics
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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
2012
Journal of Structural Biology
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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
2020
JMIR Bioinformatics and Biotechnology
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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
2015
Journal of Structural Biology
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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
2020
The EuroBiotech Journal
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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
2020
Nanoarchitectonics
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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
2006
BMC Structural Biology
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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
2004
Journal of Computational Chemistry
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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]
2019
bioRxiv
pre-print
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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
1999
Biocomputing 2000
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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
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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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