Literature DB >> 29620867

pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data.

Hiranmayi Duvvuri1,2, Lucas C Wheeler1,2, Michael J Harms1,2.   

Abstract

Here we describe pytc, an open-source Python package for global fits of thermodynamic models to multiple isothermal titration calorimetry experiments. Key features include simplicity, the ability to implement new thermodynamic models, a robust maximum likelihood fitter, a fast Bayesian Markov-Chain Monte Carlo sampler, rigorous implementation, extensive documentation, and full cross-platform compatibility. pytc fitting can be done using an application program interface or via a graphical user interface. It is available for download at https://github.com/harmslab/pytc .

Entities:  

Mesh:

Year:  2018        PMID: 29620867      PMCID: PMC5995568          DOI: 10.1021/acs.biochem.7b01264

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  15 in total

1.  Van't Hoff and calorimetric enthalpies from isothermal titration calorimetry: are there significant discrepancies?

Authors:  J R Horn; D Russell; E A Lewis; K P Murphy
Journal:  Biochemistry       Date:  2001-02-13       Impact factor: 3.162

Review 2.  Thermodynamics of protein-ligand interactions: history, presence, and future aspects.

Authors:  Remo Perozzo; Gerd Folkers; Leonardo Scapozza
Journal:  J Recept Signal Transduct Res       Date:  2004-02       Impact factor: 2.092

3.  Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein complexes in cell signaling.

Authors:  Jon C D Houtman; Patrick H Brown; Brent Bowden; Hiroshi Yamaguchi; Ettore Appella; Lawrence E Samelson; Peter Schuck
Journal:  Protein Sci       Date:  2007-01       Impact factor: 6.725

4.  Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

Authors:  Chad A Brautigam; Huaying Zhao; Carolyn Vargas; Sandro Keller; Peter Schuck
Journal:  Nat Protoc       Date:  2016-04-07       Impact factor: 13.491

5.  Evaluation of linked protonation effects in protein binding reactions using isothermal titration calorimetry.

Authors:  B M Baker; K P Murphy
Journal:  Biophys J       Date:  1996-10       Impact factor: 4.033

6.  Rapid measurement of binding constants and heats of binding using a new titration calorimeter.

Authors:  T Wiseman; S Williston; J F Brandts; L N Lin
Journal:  Anal Biochem       Date:  1989-05-15       Impact factor: 3.365

7.  Biophysical characterization of Ca2+-binding of S100A5 and Ca2+-induced interaction with RAGE.

Authors:  Iktae Kim; Ko On Lee; Young-Joo Yun; Jea Yeon Jeong; Eun-Hee Kim; Haekap Cheong; Kyoung-Seok Ryu; Nak-Kyoon Kim; Jeong-Yong Suh
Journal:  Biochem Biophys Res Commun       Date:  2016-12-23       Impact factor: 3.575

8.  Energetics of Ca(2+)-EDTA interactions: calorimetric study.

Authors:  Y V Griko
Journal:  Biophys Chem       Date:  1999-06-07       Impact factor: 2.352

Review 9.  SEDPHAT--a platform for global ITC analysis and global multi-method analysis of molecular interactions.

Authors:  Huaying Zhao; Grzegorz Piszczek; Peter Schuck
Journal:  Methods       Date:  2014-12-02       Impact factor: 3.608

10.  Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family.

Authors:  Lucas C Wheeler; Micah T Donor; James S Prell; Michael J Harms
Journal:  PLoS One       Date:  2016-10-20       Impact factor: 3.240

View more
  7 in total

1.  Learning peptide recognition rules for a low-specificity protein.

Authors:  Lucas C Wheeler; Arden Perkins; Caitlyn E Wong; Michael J Harms
Journal:  Protein Sci       Date:  2020-10-05       Impact factor: 6.725

Review 2.  Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development.

Authors:  Haixiang Yu; Obtin Alkhamis; Juan Canoura; Yingzhu Liu; Yi Xiao
Journal:  Angew Chem Int Ed Engl       Date:  2021-02-09       Impact factor: 15.336

3.  Cryo-EM structures of thermostabilized prestin provide mechanistic insights underlying outer hair cell electromotility.

Authors:  Haon Futamata; Masahiro Fukuda; Rie Umeda; Keitaro Yamashita; Atsuhiro Tomita; Satoe Takahashi; Takafumi Shikakura; Shigehiko Hayashi; Tsukasa Kusakizako; Tomohiro Nishizawa; Kazuaki Homma; Osamu Nureki
Journal:  Nat Commun       Date:  2022-10-20       Impact factor: 17.694

4.  Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms.

Authors:  Scott H Saunders; Edmund C M Tse; Matthew D Yates; Fernanda Jiménez Otero; Scott A Trammell; Eric D A Stemp; Jacqueline K Barton; Leonard M Tender; Dianne K Newman
Journal:  Cell       Date:  2020-08-06       Impact factor: 41.582

5.  Analysis of protein-ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions.

Authors:  Emil Björklund; Anna du Rietz; Patrik Lundström
Journal:  Protein Sci       Date:  2021-11-30       Impact factor: 6.725

6.  A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.

Authors:  Griffin M Schroeder; Chapin E Cavender; Maya E Blau; Jermaine L Jenkins; David H Mathews; Joseph E Wedekind
Journal:  Nat Commun       Date:  2022-01-11       Impact factor: 17.694

7.  Heterotropic roles of divalent cations in the establishment of allostery and affinity maturation of integrin αXβ2.

Authors:  Pragya Manandhar; Zahra Mazhar; Omar Abousaway; Collins Aboagye; Zeinab Moussa; Daniel Lim; Tannon Yu; James Byrnes; James M Briggs; Mehmet Sen
Journal:  Cell Rep       Date:  2022-08-23       Impact factor: 9.995

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.