Literature DB >> 32203640

Developing and applying computational resources for biochemistry education.

Paul A Craig1.   

Abstract

Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process.
© 2020 International Union of Biochemistry and Molecular Biology.

Entities:  

Keywords:  computational biology; genomics proteomics bioinformatics; integration of research into undergraduate teaching; molecular visualization; using simulation and internet resources for teaching

Mesh:

Year:  2020        PMID: 32203640      PMCID: PMC7508772          DOI: 10.1002/bmb.21347

Source DB:  PubMed          Journal:  Biochem Mol Biol Educ        ISSN: 1470-8175            Impact factor:   1.160


  20 in total

1.  EZ-Viz, a tool for simplifying molecular viewing in PyMOL.

Authors:  Laura Grell; Christopher Parkin; Len Slatest; Paul A Craig
Journal:  Biochem Mol Biol Educ       Date:  2006-11       Impact factor: 1.160

2.  Small-molecule library screening by docking with PyRx.

Authors:  Sargis Dallakyan; Arthur J Olson
Journal:  Methods Mol Biol       Date:  2015

3.  Anticipated learning outcomes for a biochemistry course-based undergraduate research experience aimed at predicting protein function from structure: Implications for assessment design.

Authors:  Stefan M Irby; Nancy J Pelaez; Trevor R Anderson
Journal:  Biochem Mol Biol Educ       Date:  2018-09       Impact factor: 1.160

4.  RASMOL: biomolecular graphics for all.

Authors:  R A Sayle; E J Milner-White
Journal:  Trends Biochem Sci       Date:  1995-09       Impact factor: 13.807

5.  The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism.

Authors:  Michael Engel; Torsten Hoffmann; Leona Wagner; Michael Wermann; Ulrich Heiser; Reiner Kiefersauer; Robert Huber; Wolfram Bode; Hans-Ulrich Demuth; Hans Brandstetter
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-10       Impact factor: 11.205

6.  GenBank.

Authors:  Dennis A Benson; Ilene Karsch-Mizrachi; Karen Clark; David J Lipman; James Ostell; Eric W Sayers
Journal:  Nucleic Acids Res       Date:  2011-12-05       Impact factor: 16.971

7.  Estimation of protein function using template-based alignment of enzyme active sites.

Authors:  Brett Hanson; Charles Westin; Mario Rosa; Alexander Grier; Mikhail Osipovitch; Madolyn L MacDonald; Greg Dodge; Paule M Boli; Cyprian W Corwin; Haeja Kessler; Talia McKay; Herbert J Bernstein; Paul A Craig
Journal:  BMC Bioinformatics       Date:  2014-03-27       Impact factor: 3.169

8.  How to Identify the Research Abilities That Instructors Anticipate Students Will Develop in a Biochemistry Course-Based Undergraduate Research Experience (CURE).

Authors:  Stefan Mark Irby; Nancy J Pelaez; Trevor R Anderson
Journal:  CBE Life Sci Educ       Date:  2018-06       Impact factor: 3.325

9.  The Pfam protein families database in 2019.

Authors:  Sara El-Gebali; Jaina Mistry; Alex Bateman; Sean R Eddy; Aurélien Luciani; Simon C Potter; Matloob Qureshi; Lorna J Richardson; Gustavo A Salazar; Alfredo Smart; Erik L L Sonnhammer; Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto; Robert D Finn
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

10.  Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

Authors:  António J M Ribeiro; Gemma L Holliday; Nicholas Furnham; Jonathan D Tyzack; Katherine Ferris; Janet M Thornton
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

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  2 in total

1.  PDB-101: Educational resources supporting molecular explorations through biology and medicine.

Authors:  Christine Zardecki; Shuchismita Dutta; David S Goodsell; Robert Lowe; Maria Voigt; Stephen K Burley
Journal:  Protein Sci       Date:  2021-10-18       Impact factor: 6.725

2.  Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab.

Authors:  Aasakiran Madamanchi; Madison Thomas; Alejandra Magana; Randy Heiland; Paul Macklin
Journal:  PRIMUS (Terre Ht)       Date:  2021-02-18
  2 in total

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