MultiSeq: unifying sequence and structure data for evolutionary analysis
Abstract
Background: Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results: Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent themore »
- Authors:
-
- Univ. of Illinois at Urbana-Champaign, IL (United States). Center for Biophysics and Computational Biology
- Univ. of Illinois at Urbana-Champaign, IL (United States). Graduate School of Library and Information Sciences
- Univ. of Illinois at Urbana-Champaign, IL (United States). Center for Biophysics and Computational Biology; Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Chemistry
- Publication Date:
- Research Org.:
- Univ. of Illinois at Urbana-Champaign, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1626326
- Grant/Contract Number:
- FG02-05ER64144
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Bioinformatics
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 1471-2105
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Mathematical & Computational Biology
Citation Formats
Roberts, Elijah, Eargle, John, Wright, Dan, and Luthey-Schulten, Zaida. MultiSeq: unifying sequence and structure data for evolutionary analysis. United States: N. p., 2006.
Web. doi:10.1186/1471-2105-7-382.
Roberts, Elijah, Eargle, John, Wright, Dan, & Luthey-Schulten, Zaida. MultiSeq: unifying sequence and structure data for evolutionary analysis. United States. https://doi.org/10.1186/1471-2105-7-382
Roberts, Elijah, Eargle, John, Wright, Dan, and Luthey-Schulten, Zaida. Wed .
"MultiSeq: unifying sequence and structure data for evolutionary analysis". United States. https://doi.org/10.1186/1471-2105-7-382. https://www.osti.gov/servlets/purl/1626326.
@article{osti_1626326,
title = {MultiSeq: unifying sequence and structure data for evolutionary analysis},
author = {Roberts, Elijah and Eargle, John and Wright, Dan and Luthey-Schulten, Zaida},
abstractNote = {Background: Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results: Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. Conclusion: MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/},
doi = {10.1186/1471-2105-7-382},
journal = {BMC Bioinformatics},
number = 1,
volume = 7,
place = {United States},
year = {Wed Aug 16 00:00:00 EDT 2006},
month = {Wed Aug 16 00:00:00 EDT 2006}
}
Works referenced in this record:
SCOP database in 2004: refinements integrate structure and sequence family data
journal, January 2004
- Andreeva, A.
- Nucleic Acids Research, Vol. 32, Issue 90001
The ASTRAL Compendium in 2004
journal, January 2004
- Chandonia, J. -M.
- Nucleic Acids Research, Vol. 32, Issue 90001
Compilation of tRNA sequences and sequences of tRNA genes
journal, January 1998
- Sprinzl, Mathias; Horn, Carsten; Brown, Melissa
- Nucleic Acids Research, Vol. 26, Issue 1, p. 148-153
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994
- Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
- Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
Protein modelling for all
journal, September 1999
- Guex, Nicolas; Diemand, Alexander; Peitsch, Manuel C.
- Trends in Biochemical Sciences, Vol. 24, Issue 9
CATH – a hierarchic classification of protein domain structures
journal, August 1997
- Orengo, Ca; Michie, Ad; Jones, S.
- Structure, Vol. 5, Issue 8
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997
- Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
- Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
The relation between the divergence of sequence and structure in proteins.
journal, April 1986
- Chothia, C.; Lesk, A. M.
- The EMBO Journal, Vol. 5, Issue 4
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
CINEMA—a novel Colour INteractive Editor for Multiple Alignments
journal, October 1998
- Parry-Smith, D. J.; Payne, A. W. R.; Michie, A. D.
- Gene, Vol. 221, Issue 1
Evolutionary profiles from the QR factorization of multiple sequence alignments
journal, March 2005
- Sethi, A.; O'Donoghue, P.; Luthey-Schulten, Z.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 11
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, December 2004
- Pruitt, K. D.
- Nucleic Acids Research, Vol. 33, Issue Database issue
DDBJ in preparation for overview of research activities behind data submissions
journal, January 2006
- Okubo, K.
- Nucleic Acids Research, Vol. 34, Issue 90001
The evolutionary history of Cys-tRNACys formation
journal, December 2005
- O'Donoghue, P.; Sethi, A.; Woese, C. R.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 52
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
journal, January 2004
- Kumar, S.
- Briefings in Bioinformatics, Vol. 5, Issue 2
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Evolutionary information for specifying a protein fold
journal, September 2005
- Socolich, Michael; Lockless, Steve W.; Russ, William P.
- Nature, Vol. 437, Issue 7058
A graph-theory algorithm for rapid protein side-chain prediction
journal, September 2003
- Canutescu, Adrian A.; Shelenkov, Andrew A.; Dunbrack, Roland L.
- Protein Science, Vol. 12, Issue 9
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
journal, December 2004
- Cole, J. R.
- Nucleic Acids Research, Vol. 33, Issue Database issue
RASMOL: biomolecular graphics for all
journal, September 1995
- Sayle, R.
- Trends in Biochemical Sciences, Vol. 20, Issue 9
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
journal, January 2003
- Boeckmann, B.
- Nucleic Acids Research, Vol. 31, Issue 1
The Diamond STING server
journal, July 2005
- Neshich, G.; Borro, L. C.; Higa, R. H.
- Nucleic Acids Research, Vol. 33, Issue Web Server
MrBayes 3: Bayesian phylogenetic inference under mixed models
journal, August 2003
- Ronquist, Fredrik; Huelsenbeck, John P.
- Bioinformatics, Vol. 19, Issue 12, p. 1572-1574
Database resources of the National Center for Biotechnology Information
journal, January 2000
- Wheeler, D. L.
- Nucleic Acids Research, Vol. 28, Issue 1
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
journal, September 2000
- Notredame, Cédric; Higgins, Desmond G.; Heringa, Jaap
- Journal of Molecular Biology, Vol. 302, Issue 1
Cn3D: sequence and structure views for Entrez
journal, June 2000
- Wang, Yanli; Geer, Lewis Y.; Chappey, Colombe
- Trends in Biochemical Sciences, Vol. 25, Issue 6
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
journal, January 2002
- Cannone, Jamie J.; Subramanian, Sankar; Schnare, Murray N.
- BMC Bioinformatics, Vol. 3, Issue 1
On the Evolution of Structure in Aminoacyl-tRNA Synthetases
journal, December 2003
- O'Donoghue, P.; Luthey-Schulten, Z.
- Microbiology and Molecular Biology Reviews, Vol. 67, Issue 4
VMD: Visual molecular dynamics
journal, February 1996
- Humphrey, William; Dalke, Andrew; Schulten, Klaus
- Journal of Molecular Graphics, Vol. 14, Issue 1
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
journal, October 1992
- Russell, Robert B.; Barton, Geoffrey J.
- Proteins: Structure, Function, and Genetics, Vol. 14, Issue 2
Multiple sequence alignments
journal, June 2005
- Wallace, Iain M.; Blackshields, Gordon; Higgins, Desmond G.
- Current Opinion in Structural Biology, Vol. 15, Issue 3
EMBL Nucleotide Sequence Database: developments in 2005
journal, January 2006
- Cochrane, G.
- Nucleic Acids Research, Vol. 34, Issue 90001
Evolutionary Profiles Derived from the QR Factorization of Multiple Structural Alignments Gives an Economy of Information
journal, February 2005
- O'Donoghue, Patrick; Luthey-Schulten, Zaida
- Journal of Molecular Biology, Vol. 346, Issue 3
Protein family annotation in a multiple alignment viewer
journal, March 2003
- Johnson, J. M.; Mason, K.; Moallemi, C.
- Bioinformatics, Vol. 19, Issue 4
Friend, an integrated analytical front-end application for bioinformatics
journal, August 2005
- Abyzov, A.; Errami, M.; Leslin, C. M.
- Bioinformatics, Vol. 21, Issue 18
Knowledge-based protein secondary structure assignment
journal, December 1995
- Frishman, Dmitrij; Argos, Patrick
- Proteins: Structure, Function, and Genetics, Vol. 23, Issue 4
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
journal, December 1997
- Thompson, J.
- Nucleic Acids Research, Vol. 25, Issue 24
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
journal, January 2003
- Cole, J. R.
- Nucleic Acids Research, Vol. 31, Issue 1
Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process
journal, March 2000
- Woese, C. R.; Olsen, G. J.; Ibba, M.
- Microbiology and Molecular Biology Reviews, Vol. 64, Issue 1
A translation approach to portable ontology specifications
journal, June 1993
- Gruber, Thomas R.
- Knowledge Acquisition, Vol. 5, Issue 2
The Jalview Java alignment editor
journal, January 2004
- Clamp, M.; Cuff, J.; Searle, S. M.
- Bioinformatics, Vol. 20, Issue 3
The integrated microbial genomes (IMG) system
journal, January 2006
- Markowitz, V. M.
- Nucleic Acids Research, Vol. 34, Issue 90001
Assessment of Protein Distance Measures and Tree-Building Methods for Phylogenetic Tree Reconstruction
journal, July 2005
- Hollich, Volker; Milchert, Lena; Arvestad, Lars
- Molecular Biology and Evolution, Vol. 22, Issue 11
Multiple Alignment of protein structures and sequences for VMD
journal, December 2005
- Eargle, John; Wright, Dan; Luthey-Schulten, Zaida
- Bioinformatics, Vol. 22, Issue 4
Evolutionary trees from DNA sequences: A maximum likelihood approach
journal, November 1981
- Felsenstein, Joseph
- Journal of Molecular Evolution, Vol. 17, Issue 6
Summary: the modified nucleosides of RNA
journal, January 1994
- Limbach, Patrick A.; Crain, Pamela F.; McCloskey, James A.
- Nucleic Acids Research, Vol. 22, Issue 12
Comparative Protein Structure Modeling of Genes and Genomes
journal, June 2000
- Martí-Renom, Marc A.; Stuart, Ashley C.; Fiser, András
- Annual Review of Biophysics and Biomolecular Structure, Vol. 29, Issue 1
MollDE: a homology modeling framework you can click with
journal, April 2005
- Canutescu, A. A.; Dunbrack, R. L.
- Bioinformatics, Vol. 21, Issue 12
Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases
journal, December 2001
- Al-Lazikani, B.; Sheinerman, F. B.; Honig, B.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 26
Evaluating protein structure-prediction schemes using energy landscape theory
journal, May 2001
- Eastwood, M. P.; Hardin, C.; Luthey-Schulten, Z.
- IBM Journal of Research and Development, Vol. 45, Issue 3.4
A standard reference frame for the description of nucleic acid base-pair geometry 1 1Edited by P. E. Wright 2 2This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.
journal, October 2001
- Olson, Wilma K.; Bansal, Manju; Burley, Stephen K.
- Journal of Molecular Biology, Vol. 313, Issue 1
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
journal, September 1992
- Berman, H. M.; Olson, W. K.; Beveridge, D. L.
- Biophysical Journal, Vol. 63, Issue 3
The relation between the divergence of sequence and structure in proteins.
journal, April 1986
- Chothia, C.; Lesk, A. M.
- The EMBO Journal, Vol. 5, Issue 4
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
journal, October 1992
- Russell, Robert B.; Barton, Geoffrey J.
- Proteins: Structure, Function, and Genetics, Vol. 14, Issue 2
A standard reference frame for the description of nucleic acid base-pair geometry 1 1Edited by P. E. Wright 2 2This is a document of the Nomenclature Committee of IUBMB (NC-IUBMB)/IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN), whose members are R. Cammack (chairman), A. Bairoch, H.M. Berman, S. Boyce, C.R. Cantor, K. Elliott, D. Horton, M. Kanehisa, A. Kotyk, G.P. Moss, N. Sharon and K.F. Tipton.
journal, October 2001
- Olson, Wilma K.; Bansal, Manju; Burley, Stephen K.
- Journal of Molecular Biology, Vol. 313, Issue 1
A translation approach to portable ontology specifications
journal, June 1993
- Gruber, Thomas R.
- Knowledge Acquisition, Vol. 5, Issue 2
Comparative analyses of the mitochondrial genomes of the cattle tick Rhipicephalus microplus clades A and B from China
journal, April 2022
- Deng, Yuan-Ping; Yi, Jia-Ning; Fu, Yi-Tian
- Parasitology Research, Vol. 121, Issue 6
Molecular and biological characterization of an isolate of the potyvirus passiflora virus Y naturally infecting soybean (Glycine max) in Brazil
journal, September 2022
- Ribeiro-Junior, Marcos Roberto; Barreto da Silva, Felipe; Marubayashi, Julio Massaharu
- Archives of Virology, Vol. 167, Issue 12
Evolutionary Profiles Derived from the QR Factorization of Multiple Structural Alignments Gives an Economy of Information
journal, February 2005
- O'Donoghue, Patrick; Luthey-Schulten, Zaida
- Journal of Molecular Biology, Vol. 346, Issue 3
Multiple sequence alignments
journal, June 2005
- Wallace, Iain M.; Blackshields, Gordon; Higgins, Desmond G.
- Current Opinion in Structural Biology, Vol. 15, Issue 3
Which craft is best in bioinformatics?
journal, July 2001
- Attwood, T. K.; Miller, C. J.
- Computers & Chemistry, Vol. 25, Issue 4
Evolutionary information for specifying a protein fold
journal, September 2005
- Socolich, Michael; Lockless, Steve W.; Russ, William P.
- Nature, Vol. 437, Issue 7058
Codon-optimized FAM132b gene therapy prevents dietary obesity by blockading adrenergic response and insulin action
journal, August 2022
- Qi, Zhengtang; Xia, Jie; Xue, Xiangli
- International Journal of Obesity, Vol. 46, Issue 11
Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62
journal, January 2021
- Itskanov, Samuel; Kuo, Katie M.; Gumbart, James C.
- Nature Structural & Molecular Biology, Vol. 28, Issue 2
Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases
journal, December 2001
- Al-Lazikani, B.; Sheinerman, F. B.; Honig, B.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 26
Evolutionary profiles from the QR factorization of multiple sequence alignments
journal, March 2005
- Sethi, A.; O'Donoghue, P.; Luthey-Schulten, Z.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 11
The evolutionary history of Cys-tRNACys formation
journal, December 2005
- O'Donoghue, P.; Sethi, A.; Woese, C. R.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 52
Protein family annotation in a multiple alignment viewer
journal, March 2003
- Johnson, J. M.; Mason, K.; Moallemi, C.
- Bioinformatics, Vol. 19, Issue 4
MollDE: a homology modeling framework you can click with
journal, April 2005
- Canutescu, A. A.; Dunbrack, R. L.
- Bioinformatics, Vol. 21, Issue 12
Friend, an integrated analytical front-end application for bioinformatics
journal, August 2005
- Abyzov, A.; Errami, M.; Leslin, C. M.
- Bioinformatics, Vol. 21, Issue 18
Summary: the modified nucleosides of RNA
journal, January 1994
- Limbach, Patrick A.; Crain, Pamela F.; McCloskey, James A.
- Nucleic Acids Research, Vol. 22, Issue 12
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994
- Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
- Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997
- Lowe, Todd M.; Eddy, Sean R.
- Nucleic Acids Research, Vol. 25, Issue 5
Database resources of the National Center for Biotechnology Information
journal, January 2001
- Wheeler, D. L.
- Nucleic Acids Research, Vol. 29, Issue 1
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
journal, January 2003
- Cole, J. R.
- Nucleic Acids Research, Vol. 31, Issue 1
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
journal, January 2003
- Boeckmann, B.
- Nucleic Acids Research, Vol. 31, Issue 1
SCOP database in 2004: refinements integrate structure and sequence family data
journal, January 2004
- Andreeva, A.
- Nucleic Acids Research, Vol. 32, Issue 90001
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, December 2004
- Pruitt, K. D.
- Nucleic Acids Research, Vol. 33, Issue Database issue
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
journal, December 2004
- Cole, J. R.
- Nucleic Acids Research, Vol. 33, Issue Database issue
The Diamond STING server
journal, July 2005
- Neshich, G.; Borro, L. C.; Higa, R. H.
- Nucleic Acids Research, Vol. 33, Issue Web Server
The integrated microbial genomes (IMG) system
journal, January 2006
- Markowitz, V. M.
- Nucleic Acids Research, Vol. 34, Issue 90001
DDBJ in preparation for overview of research activities behind data submissions
journal, January 2006
- Okubo, K.
- Nucleic Acids Research, Vol. 34, Issue 90001
EMBL Nucleotide Sequence Database: developments in 2005
journal, January 2006
- Cochrane, G.
- Nucleic Acids Research, Vol. 34, Issue 90001
A graph-theory algorithm for rapid protein side-chain prediction
journal, September 2003
- Canutescu, Adrian A.; Shelenkov, Andrew A.; Dunbrack, Roland L.
- Protein Science, Vol. 12, Issue 9
Comparative Protein Structure Modeling of Genes and Genomes
journal, June 2000
- Martí-Renom, Marc A.; Stuart, Ashley C.; Fiser, András
- Annual Review of Biophysics and Biomolecular Structure, Vol. 29, Issue 1
Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase
text, January 2020
- Radon, Christin; Mittelstädt, Gerd; Duffus, Benjamin R.
- Freie Universität Berlin
Works referencing / citing this record:
Single‐molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase
journal, March 2017
- Lin, Chang‐Ting; Tritschler, Felix; Lee, Kyung Suk
- Protein Science, Vol. 26, Issue 7
Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε
journal, February 2019
- Hardianto, Ari; Khanna, Varun; Liu, Fei
- BMC Bioinformatics, Vol. 19, Issue S13
All-atom molecular dynamics comparison of disease-associated zinc fingers
text, January 2017
- Godwin, Ryan C.; Gmeiner, William H.; Salsbury, Freddie R.
- Figshare
Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions
journal, November 2014
- Scherer, Myriam; Klingl, Stefan; Sevvana, Madhumati
- PLoS Pathogens, Vol. 10, Issue 11
Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants
journal, September 2018
- Liou, Geoffrey; Chiang, Ying-Chih; Wang, Yi
- The Journal Of Biological Chemistry
Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting
journal, April 2019
- Okazaki, Kei-ichi; Wöhlert, David; Warnau, Judith
- Nature Communications, Vol. 10, Issue 1
Pathways to disease from natural variations in human cytoplasmic tRNAs
journal, April 2019
- Lant, Jeremy T.; Berg, Matthew D.; Heinemann, Ilka U.
- Journal of Biological Chemistry, Vol. 294, Issue 14
Dynamical networks in tRNA:protein complexes
journal, April 2009
- Sethi, A.; Eargle, J.; Black, A. A.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 16
Protein–protein interactions within photosystem II under photoprotection: the synergy between CP29 minor antenna, subunit S (PsbS) and zeaxanthin at all-atom resolution
journal, January 2018
- Daskalakis, Vangelis
- Physical Chemistry Chemical Physics, Vol. 20, Issue 17
Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox‐based modifications
journal, June 2019
- Castro‐Torres, Eduardo; Jiménez‐Sandoval, Pedro; Romero‐Romero, Sergio
- The Plant Journal, Vol. 99, Issue 5
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
journal, January 2012
- Diemer, Geoffrey S.; Stedman, Kenneth M.
- Biology Direct, Vol. 7, Issue 1
Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations
journal, March 2020
- Houndonougbo, Yao; Pugh, Bethany; VanWormer, Kandise
- Journal of Biomolecular Structure and Dynamics, Vol. 39, Issue 4
The TATA‐binding Protein DNA‐binding domain of eukaryotic parasites is a potentially druggable target
journal, October 2019
- Santiago, Ángel; Razo‐Hernández, Rodrigo Said; Pastor, Nina
- Chemical Biology & Drug Design, Vol. 95, Issue 1
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation
journal, June 2007
- Kavran, J. M.; Gundllapalli, S.; O'Donoghue, P.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 27
Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways
journal, November 2018
- Hermann, Johannes; Nowotny, Phillip; Schrader, Tobias E.
- Acta Crystallographica Section F Structural Biology Communications, Vol. 74, Issue 12
GASP‐1 and GASP‐2, two closely structurally related proteins with a functional duality in antitrypsin inhibition specificity: a mechanistic point of view
journal, October 2019
- Parenté, Alexis; Di Meo, Florent; Lapeyronie, Eric
- The FEBS Journal, Vol. 287, Issue 5
A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection
journal, February 2019
- Wright, Shane C.; Kozielewicz, Paweł; Kowalski-Jahn, Maria
- Nature Communications, Vol. 10, Issue 1
Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights
journal, November 2018
- Hong, Lu; Vani, Bodhi P.; Thiede, Erik H.
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 49
Coupling between an electrostatic network and the Zn2+ binding site modulates Hv1 activation
journal, May 2018
- De La Rosa, Victor; Bennett, Ashley L.; Ramsey, Ian Scott
- Journal of General Physiology, Vol. 150, Issue 6
The high-affinity calcium sensor synaptotagmin-7 serves multiple roles in regulated exocytosis
journal, May 2018
- MacDougall, Daniel D.; Lin, Zesen; Chon, Nara L.
- Journal of General Physiology, Vol. 150, Issue 6
Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity
journal, January 2019
- Dzimianski, John V.; Beldon, Brianna S.; Daczkowski, Courtney M.
- PLOS Pathogens, Vol. 15, Issue 1
The Crystal Structure of Human Soluble CD14 Reveals a Bent Solenoid with a Hydrophobic Amino-Terminal Pocket
journal, December 2012
- Kelley, Stacy L.; Lukk, Tiit; Nair, Satish K.
- The Journal of Immunology, Vol. 190, Issue 3
Bifunctional ADP-dependent phosphofructokinase/glucokinase activity in the order Methanococcales - biochemical characterization of the mesophilic enzyme from Methanococcus maripaludis
journal, March 2014
- Castro-Fernandez, Victor; Bravo-Moraga, Felipe; Herrera-Morande, Alejandra
- FEBS Journal, Vol. 281, Issue 8
Functional divergence between evolutionary‐related LuxG and Fre oxidoreductases of luminous bacteria
journal, April 2019
- Deeva, Anna A.; Zykova, Evgenia A.; Nemtseva, Elena V.
- Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 9
Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme
journal, January 2012
- Su, Dan; Ojo, Temitope T.; Söll, Dieter
- FEBS Letters, Vol. 586, Issue 6
Gld2 activity is regulated by phosphorylation in the N-terminal domain
text, January 2019
- Chung, Christina Z.; Balasuriya, Nileeka; Manni, Emad
- Taylor & Francis
Gld2 activity is regulated by phosphorylation in the N-terminal domain
journal, May 2019
- Chung, Christina Z.; Balasuriya, Nileeka; Manni, Emad
- RNA Biology, Vol. 16, Issue 8
Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori
journal, August 2016
- Pandey, Preeti; Tarique, Khaja Faisal; Mazumder, Mohit
- Scientific Reports, Vol. 6, Issue 1
Gld2 activity is regulated by phosphorylation in the N-terminal domain
text, January 2020
- Chung, Christina Z.; Balasuriya, Nileeka; Manni, Emad
- Taylor & Francis
Evidence for a Non-Catalytic Ion-Binding Site in Multiple RNA-Dependent RNA Polymerases
journal, July 2012
- Mönttinen, Heli A. M.; Ravantti, Janne J.; Poranen, Minna M.
- PLoS ONE, Vol. 7, Issue 7
All-atom molecular dynamics comparison of disease-associated zinc fingers
text, January 2017
- Godwin, Ryan C.; Gmeiner, William H.; Salsbury, Freddie R.
- Figshare
Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
journal, October 2018
- Chiang, Ying-Chih; Levsh, Olesya; Lam, Chun Kei
- PLOS Computational Biology, Vol. 14, Issue 10
A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans
journal, January 2018
- Jaña, Gonzalo A.; Mendoza, Fernanda; Osorio, Manuel I.
- Organic & Biomolecular Chemistry, Vol. 16, Issue 14
Structure and function of Toll/interleukin-1 receptor/resistance protein (TIR) domains
journal, December 2014
- Ve, Thomas; Williams, Simon J.; Kobe, Bostjan
- Apoptosis, Vol. 20, Issue 2
Molecular model of human heparanase with proposed binding mode of a heparan sulfate oligosaccharide and catalytic amino acids
journal, July 2011
- Sapay, Nicolas; Cabannes, Éric; Petitou, Maurice
- Biopolymers, Vol. 97, Issue 1
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation
journal, July 2010
- Nureki, Osamu; O’Donoghue, Patrick; Watanabe, Nobuhisa
- Nucleic Acids Research, Vol. 38, Issue 20
The first plant acyl-CoA-binding protein structures: the close homologues OsACBP1 and OsACBP2 from rice
journal, April 2017
- Guo, Ze-Hua; Chan, Wallace H. Y.; Kong, Geoffrey K. W.
- Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 5
Effect of catalytic subunit phosphorylation on the properties of SnRK1 from Phaseolus vulgaris embryos
journal, July 2018
- Zúñiga-Sánchez, Esther; Rodríguez-Sotres, Rogelio; Coello, Patricia
- Physiologia Plantarum, Vol. 165, Issue 3
Structure functional insights into calcium binding during the activation of coagulation factor XIII A
journal, August 2019
- Singh, Sneha; Dodt, Johannes; Volkers, Peter
- Scientific Reports, Vol. 9, Issue 1
Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations
journal, May 2012
- Hsin, J.; Gopinathan, A.; Huang, K. C.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 24
Genome-Wide Identification and Evolution of HECT Genes in Soybean
journal, April 2015
- Meng, Xianwen; Wang, Chen; Rahman, Siddiq
- International Journal of Molecular Sciences, Vol. 16, Issue 12
Histone H2A and H4 N-terminal Tails Are Positioned by the MEP50 WD Repeat Protein for Efficient Methylation by the PRMT5 Arginine Methyltransferase
journal, April 2015
- Burgos, Emmanuel S.; Wilczek, Carola; Onikubo, Takashi
- Journal of Biological Chemistry, Vol. 290, Issue 15
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation
journal, January 2008
- Sherrer, R. Lynn; O’Donoghue, Patrick; Söll, Dieter
- Nucleic Acids Research, Vol. 36, Issue 4, p. 1247-1259
Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations
text, January 2020
- Houndonougbo, Yao; Pugh, Bethany; VanWormer, Kandise
- Taylor & Francis
Atomistic probing of aptameric binding of CD19 outer membrane domain reveals an “aptamer walking” mechanism
journal, January 2020
- Danquah, Michael K.; Guo, Hao‐Bo; Tan, Kei X.
- Biotechnology Progress, Vol. 36, Issue 3
Profiling the interaction of 1‐phenylbenzimidazoles to cyclooxygenases
journal, July 2019
- Gómez‐Castro, Carlos Z.; López‐Martínez, Margarita; Hernández‐Pineda, Jessica
- Journal of Molecular Recognition, Vol. 32, Issue 11
Fine-tuned preparation of cross-linked laccase nanoaggregates
journal, May 2019
- Şahutoğlu, Arif Sercan; Akgül, Cahit
- Biocatalysis and Biotransformation, Vol. 37, Issue 6
Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
journal, May 2012
- Vijayabaskar, M. S.; Vishveshwara, Saraswathi
- PLoS Computational Biology, Vol. 8, Issue 5
Mapping of heparin/heparan sulfate binding sites on αvβ3 integrin by molecular docking: HEPARIN - αvβ3 INTEGRIN COMPLEX
journal, January 2013
- Ballut, Lionel; Sapay, Nicolas; Chautard, Émilie
- Journal of Molecular Recognition, Vol. 26, Issue 2
Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants
journal, November 2018
- Liou, Geoffrey; Chiang, Ying-Chih; Wang, Yi
- Journal of Biological Chemistry, Vol. 293, Issue 48
NetworkView: 3D display and analysis of protein{middle dot}RNA interaction networks
journal, September 2012
- Eargle, J.; Luthey-Schulten, Z.
- Bioinformatics, Vol. 28, Issue 22
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
text, January 2016
- Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben
- Deutsches Elektronen-Synchrotron, DESY, Hamburg
Static Clathrin Assemblies at the Peripheral Vacuole-Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia.
text, January 2016
- Zumthor, Jon Paulin; Cernikova, Lenka; Rout, Samuel
- Public Library of Science
Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification
journal, March 2018
- Boisclair Lachance, Jean-François; Webber, Jemma L.; Hong, Lu
- Genes & Development, Vol. 32, Issue 5-6
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
journal, June 2018
- Fang, Xin; Monk, Jonathan M.; Mih, Nathan
- BMC Systems Biology, Vol. 12, Issue 1
Long distance electron transfer through the aqueous solution between redox partner proteins
journal, December 2018
- Lagunas, Anna; Guerra-Castellano, Alejandra; Nin-Hill, Alba
- Nature Communications, Vol. 9, Issue 1
Identification and characterization of NF-YB family genes in tung tree
journal, June 2015
- Yang, Susu; Wang, Yangdong; Yin, Hengfu
- Molecular Genetics and Genomics, Vol. 290, Issue 6
Crystal structure and its bearing towards an understanding of key biological functions of EpCAM
journal, August 2014
- Pavšič, Miha; Gunčar, Gregor; Djinović-Carugo, Kristina
- Nature Communications, Vol. 5, Issue 1
Approaches for Designing new Potent Inhibitors of Farnesyl Pyrophosphate Synthase
journal, February 2016
- Rodriguez, Juan B.; Falcone, Bruno N.; Szajnman, Sergio H.
- Expert Opinion on Drug Discovery, Vol. 11, Issue 3
Electron cryo-microscopy structure of the canonical TRPC4 ion channel
journal, May 2018
- Vinayagam, Deivanayagabarathy; Mager, Thomas; Apelbaum, Amir
- eLife, Vol. 7
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
journal, July 2016
- Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben
- Journal of Biological Chemistry, Vol. 291, Issue 28
Gld2 activity is regulated by phosphorylation in the N-terminal domain
text, January 2020
- Chung, Christina Z.; Balasuriya, Nileeka; Manni, Emad
- Taylor & Francis
Measles Virus Bearing Measles Inclusion Body Encephalitis-Derived Fusion Protein Is Pathogenic after Infection via the Respiratory Route
journal, February 2019
- Mathieu, Cyrille; Ferren, Marion; Jurgens, Eric
- Journal of Virology, Vol. 93, Issue 8
Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis
journal, July 2019
- Barruetabeña, Nerea; Alonso-Lerma, Borja; Galera-Prat, Albert
- Communications Chemistry, Vol. 2, Issue 1
All-atom molecular dynamics comparison of disease-associated zinc fingers
journal, August 2017
- Godwin, Ryan C.; Gmeiner, William H.; Salsbury, Freddie R.
- Journal of Biomolecular Structure and Dynamics, Vol. 36, Issue 10
Structural dynamics of inosine triphosphate pyrophosphatase (ITPA) protein and two clinically relevant mutants: molecular dynamics simulations
text, January 2020
- Houndonougbo, Yao; Pugh, Bethany; VanWormer, Kandise
- Taylor & Francis
Structures of the prefusion form of measles virus fusion protein in complex with inhibitors
journal, February 2018
- Hashiguchi, Takao; Fukuda, Yoshinari; Matsuoka, Rei
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 10
Static Clathrin Assemblies at the Peripheral Vacuole—Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia
journal, July 2016
- Zumthor, Jon Paulin; Cernikova, Lenka; Rout, Samuel
- PLOS Pathogens, Vol. 12, Issue 7
Identification of sesquiterpene synthases from the Basidiomycota Coniophora puteana for the efficient and highly selective β-copaene and cubebol production in E. coli
journal, October 2018
- Mischko, Wolfgang; Hirte, Max; Fuchs, Monika
- Microbial Cell Factories, Vol. 17, Issue 1
Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites
journal, May 2011
- Li, L.; Boniecki, M. T.; Jaffe, J. D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 23
Biogenesis of cytochrome c oxidase — in vitro approaches to study cofactor insertion into a bacterial subunit I
journal, July 2008
- Greiner, Peter; Hannappel, Achim; Werner, Carolin
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1777, Issue 7-8
Structural Determinants of Cadherin-23 Function in Hearing and Deafness
journal, January 2010
- Sotomayor, Marcos M.; Weihofen, Wilhelm; Gaudet, Rachelle
- Biophysical Journal, Vol. 98, Issue 3
Theoretical and Computational Investigation of Flagellin Translocation and Bacterial Flagellum Growth
journal, June 2011
- Tanner, David E.; Ma, Wen; Chen, Zhongzhou
- Biophysical Journal, Vol. 100, Issue 11
Conformational Coupling of the Nucleotide-Binding and the Transmembrane Domains in ABC Transporters
journal, August 2011
- Wen, Po-Chao; Tajkhorshid, Emad
- Biophysical Journal, Vol. 101, Issue 3
Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme
journal, January 2012
- Su, Dan; Ojo, Temitope T.; Söll, Dieter
- FEBS Letters, Vol. 586, Issue 6
Can all heritable biology really be reduced to a single dimension?
journal, March 2016
- Babbitt, Gregory A.; Coppola, Erin E.; Alawad, Mohammed A.
- Gene, Vol. 578, Issue 2
A structural analysis of the AAA+ domains in Saccharomyces cerevisiae cytoplasmic dynein
journal, June 2014
- Gleave, Emma S.; Schmidt, Helgo; Carter, Andrew P.
- Journal of Structural Biology, Vol. 186, Issue 3
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB
journal, January 2020
- Shin, Donghyuk; Mukherjee, Rukmini; Liu, Yaobin
- Molecular Cell, Vol. 77, Issue 1
Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations
journal, December 2019
- Cheng, Mary Hongying; Ponzoni, Luca; Sorkina, Tatiana
- Neuropharmacology, Vol. 161
Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants
journal, May 2016
- Durrant, Jacob D.; Bush, Robin M.; Amaro, Rommie E.
- The Journal of Physical Chemistry B, Vol. 120, Issue 33
Src activation by β-adrenoreceptors is a key switch for tumour metastasis
journal, January 2013
- Armaiz-Pena, Guillermo N.; Allen, Julie K.; Cruz, Anthony
- Nature Communications, Vol. 4, Issue 1
A pathway for protective quenching in antenna proteins of Photosystem II
journal, May 2017
- Papadatos, Sotiris; Charalambous, Antreas C.; Daskalakis, Vangelis
- Scientific Reports, Vol. 7, Issue 1
Search for non-lactam inhibitors of mtb β-lactamase led to its open shape in apo state: new concept for antibiotic design
journal, July 2017
- Sagar, Amin; Haleem, Nazia; Bashir, Yaawar Mir
- Scientific Reports, Vol. 7, Issue 1
Structure functional insights into calcium binding during the activation of coagulation factor XIII A
journal, August 2019
- Singh, Sneha; Dodt, Johannes; Volkers, Peter
- Scientific Reports, Vol. 9, Issue 1
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases
journal, July 2016
- Valencia-Sánchez, Marco Igor; Rodríguez-Hernández, Annia; Ferreira, Ruben
- Journal of Biological Chemistry, Vol. 291, Issue 28
Comparative sequence analysis suggests a conserved gating mechanism for TRP channels
journal, June 2015
- Palovcak, Eugene; Delemotte, Lucie; Klein, Michael L.
- Journal of General Physiology, Vol. 146, Issue 1
Coupling between an electrostatic network and the Zn2+ binding site modulates Hv1 activation
journal, May 2018
- De La Rosa, Victor; Bennett, Ashley L.; Ramsey, Ian Scott
- Journal of General Physiology, Vol. 150, Issue 6
Boulder ALignment Editor (ALE): a web-based RNA alignment tool
journal, May 2011
- Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel
- Bioinformatics, Vol. 27, Issue 12
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation
journal, December 2007
- Araiso, Y.; Palioura, S.; Ishitani, R.
- Nucleic Acids Research, Vol. 36, Issue 4
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation
journal, January 2008
- Sherrer, R. Lynn; O’Donoghue, Patrick; Söll, Dieter
- Nucleic Acids Research, Vol. 36, Issue 4, p. 1247-1259
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation
journal, July 2010
- Nureki, Osamu; O’Donoghue, Patrick; Watanabe, Nobuhisa
- Nucleic Acids Research, Vol. 38, Issue 20
The Molecular Dynamics ofTrypanosoma bruceiUDP‐Galactose 4′‐Epimerase: A Drug Target for African Sleeping Sickness
journal, May 2012
- Friedman, Aaron J.; Durrant, Jacob D.; Pierce, Levi C. T.
- Chemical Biology & Drug Design, Vol. 80, Issue 2
Flexible mapping of homology onto structure with Homolmapper
journal, April 2007
- Rockwell, Nathan C.; Lagarias, J. Clark
- BMC Bioinformatics, Vol. 8, Issue 1
Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4
journal, January 2009
- Chen, Ke; Roberts, Elijah; Luthey-Schulten, Zaida
- BMC Evolutionary Biology, Vol. 9, Issue 1
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA
journal, January 2011
- Rostkowski, Michał; Olsson, Mats HM; Søndergaard, Chresten R.
- BMC Structural Biology, Vol. 11, Issue 1
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
journal, January 2012
- Diemer, Geoffrey S.; Stedman, Kenneth M.
- Biology Direct, Vol. 7, Issue 1
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
journal, June 2018
- Fang, Xin; Monk, Jonathan M.; Mih, Nathan
- BMC Systems Biology, Vol. 12, Issue 1
Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex
journal, October 2011
- Sethi, Anurag; Goldstein, Byron; Gnanakaran, S.
- PLoS Computational Biology, Vol. 7, Issue 10
Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
journal, January 2013
- Yu, Hang; Schulten, Klaus
- PLoS Computational Biology, Vol. 9, Issue 1
Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs
journal, December 2013
- Blachly, Patrick G.; de Oliveira, César A. F.; Williams, Sarah L.
- PLoS Computational Biology, Vol. 9, Issue 12
X-Ray Structure Reveals a New Class and Provides Insight into Evolution of Alkaline Phosphatases
journal, July 2011
- Bihani, Subhash C.; Das, Amit; Nilgiriwala, Kayzad S.
- PLoS ONE, Vol. 6, Issue 7
Conformational Stability Analyses of Alpha Subunit I Domain of LFA-1 and Mac-1
journal, August 2011
- Mao, Debin; Lü, Shouqin; Li, Ning
- PLoS ONE, Vol. 6, Issue 8
Evidence for a Non-Catalytic Ion-Binding Site in Multiple RNA-Dependent RNA Polymerases
journal, July 2012
- Mönttinen, Heli A. M.; Ravantti, Janne J.; Poranen, Minna M.
- PLoS ONE, Vol. 7, Issue 7
Characterization of Danio rerio Mn2+-Dependent ADP-Ribose/CDP-Alcohol Diphosphatase, the Structural Prototype of the ADPRibase-Mn-Like Protein Family
journal, July 2012
- Rodrigues, Joaquim Rui; Fernández, Ascensión; Canales, José
- PLoS ONE, Vol. 7, Issue 7
Exploring PHD Fingers and H3K4me0 Interactions with Molecular Dynamics Simulations and Binding Free Energy Calculations: AIRE-PHD1, a Comparative Study
journal, October 2012
- Spiliotopoulos, Dimitrios; Spitaleri, Andrea; Musco, Giovanna
- PLoS ONE, Vol. 7, Issue 10
Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis
journal, June 2013
- Rivas-Pardo, Jaime Andrés; Herrera-Morande, Alejandra; Castro-Fernandez, Victor
- PLoS ONE, Vol. 8, Issue 6
Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
journal, August 2013
- Cashman, Derek J.; Ortega, Davi R.; Zhulin, Igor B.
- PLoS ONE, Vol. 8, Issue 8
Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases
journal, May 2015
- Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda
- PLOS ONE, Vol. 10, Issue 5
Characterization and expression analysis of Galnts in developing Strongylocentrotus purpuratus embryos
journal, April 2017
- Famiglietti, Amber L.; Wei, Zheng; Beres, Thomas M.
- PLOS ONE, Vol. 12, Issue 4
Linking epigenetic function to electrostatics: The DNMT2 structural model example
journal, June 2017
- Vieira, Gilberto Cavalheiro; Vieira, Gustavo Fioravanti; Sinigaglia, Marialva
- PLOS ONE, Vol. 12, Issue 6
Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity
journal, January 2019
- Dzimianski, John V.; Beldon, Brianna S.; Daczkowski, Courtney M.
- PLOS Pathogens, Vol. 15, Issue 1
Comparative genomic analyses of the cyanobacterium, Lyngbya aestuarii BL J, a powerful hydrogen producer
journal, January 2013
- Kothari, Ankita
- Frontiers in Microbiology, Vol. 4
Antifungal Activity against Filamentous Fungi of Ts1, a Multifunctional Toxin from Tityus serrulatus Scorpion Venom
journal, June 2017
- Santussi, Welligton M.; Bordon, Karla C. F.; Rodrigues Alves, Ana P. N.
- Frontiers in Microbiology, Vol. 8
Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling
journal, February 2015
- Aguayo, M. Francisca; Cáceres, Juan Carlos; Fuentealba, MatÃas
- Frontiers in Plant Science, Vol. 6
A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases
journal, June 2017
- Cheng, Kevin; Demir, Özlem; Amaro, Rommie
- Genes, Vol. 8, Issue 6
Genome-Wide Identification and Evolution of HECT Genes in Soybean
journal, April 2015
- Meng, Xianwen; Wang, Chen; Rahman, Siddiq
- International Journal of Molecular Sciences, Vol. 16, Issue 12
Studying RNA homology and conservation with Infernal: from single sequences to RNA families
preprint, January 2012
- Barquist, Lars; Burge, Sarah W.; Gardner, Paul P.
- arXiv
From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles Through Computation
journal, September 2012
- Wymore, Troy; Brooks, Charles L.
- Computational and Structural Biotechnology Journal, Vol. 2, Issue 3
Annotation of gene sequence and protein structure of brinjal EDS1
journal, March 2017
- Sharma, Soumya; Jaiswal, Sarika
- Bioinformation, Vol. 13, Issue 03
Proton currents constrain structural models of voltage sensor activation
journal, August 2016
- Randolph, Aaron L.; Mokrab, Younes; Bennett, Ashley L.
- eLife, Vol. 5
Static Clathrin Assemblies at the Peripheral Vacuole-Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia.
text, January 2016
- Zumthor, Jon Paulin; Cernikova, Lenka; Rout, Samuel
- Public Library of Science