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THESEUS - Maximum likelihood superpositioning and analysis of macromolecular structuresTheobald Lab web page
http://www.theseus3d.org/
Theobald Lab web page
http://www.theseus3d.org/
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Brandeis University
Douglas Theobald
MS 009,●●●●●●●outh St
Wa●●am , MA, 02454-9110
US
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Brandeis University
Douglas Theobald
MS 009,●●●●●●●outh St
Wa●●am , MA, 02454-9110
US
View this contact
Brandeis University
Douglas Theobald
MS 009,●●●●●●●outh St
Wa●●am , MA, 02454-9110
US
View this contact
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THESEUS - Maximum likelihood superpositioning and analysis of macromolecular structures | theseus3d.org Reviews
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Theobald Lab web page
Theobald Lab: Publications
http://theobald.brandeis.edu/publications.html
Waltham, MA 02453. Theobald lab publications at PubMed. Erin L. Devine, Douglas L. Theobald, and Daniel D. Oprian (2016). Relocating the active-site lysine in rhodopsin: 2. Evolutionary intermediates.". Doi:10.1021/acs.biochem.6b00478. Phillip A. Steindel, Emily H. Chen, Jacob D. Wirth, and Douglas L. Theobald (2016). Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases.". 25(7):1319-1331. [ Open Access. Douglas L. Theobald (2016). Kristine A. Mack...
Theobald Lab: QCP Method
http://theobald.brandeis.edu/qcp
The QCP Superposition Method. Waltham, MA 02453. The Quaternion Characteristic Polynomial method: Ultrafast determination of the minimum RMSD and the optimal least-squares rotation matrix. Method avoids the costly matrix decomposition by taking advantage of special properties of the quaternion representation of rotations and of the characteristic polynomial of the 4×4 "key" matrix. If the optimal rotation matrix is also desired, then the best rotation is given by the corresponding eigenvector, which we c...
Bosco K Ho's Emporium - Structural alignment done right
http://boscoh.com/protein/structural-alignment-done-right.html
Bosco K. Ho's. Peddling the Frenzied Recollections of an. Structural alignment done right. What is it to be alike? When you're talking about protein structures, you need to align the structures as best you can before you can talk about similarity. This is not a trivial matter. The standard approach is to use the Kabsch RMSD algorithm. To find the optimal superposition between two sets of coordinates. Except you don't need to fudge it anymore! Flag means take only a single conformation from each PDB file:.
Theobald Lab:People
http://theobald.brandeis.edu/people.html
Waltham, MA 02453. Douglas L. Theobald. Waltham, MA 02454. The lab, with the lovely historic Brandeis Usen Castle in background, August 2, 2013. Left to right: Rick Roy, Erin Devine, Brian Beckett, Joe Jacobowitz, Kristine Mackin, Jeff Boucher, Phil Steindel, Douglas Theobald. Brian C. Beckett. Rick works on understanding the functional and structural constraints on universally conserved residues in Type I rhodopsins. Erin Devine, PhD. Michelle Y. Fry (2015). Kristine Mackin, PhD. Kristine's thesis proje...
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THESEUS - Maximum likelihood superpositioning and analysis of macromolecular structures
MS 009, 415 South St. Waltham, MA 02454. A program for maximum likelihood superpositioning and analysis of macromolecular structures. Is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus. When superposing macromolecules with different residue sequences, other programs and algorithms discard residues that are aligned with gaps. Theseus. Linked below), that calls Theseus. A conventional least-squares superpositio...
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