Research Interests: Evolution, Biochemistry, and Human Genetics

• dissertation.final.pdf - the dissertation itself, in .pdf format
• alignment database - the most recent version of this is the CCAPD (Consolidated Curated Alignments for Phylogenetics Database)
• altered PDB files for alignments
• analyses of matrices versus structural alignments
• old version of this page, with more on human genetics, etc.
• legalcode.txt for the licensing terms this page and most material under it are under
• A patched version (lsqrms-2.0.4b.patched.tar.bz2) of LSQRMS, used for structural alignments; alternatively, see lsqrms-2.0.4b.patched.tar.gz
• mdp files used for running GROMACS (a reference on the format is at http://www.gromacs.org/documentation/reference/online/mdp_opt.html)
• Results of running MolProbity on various structures, plus some analysis
• patches to existing programs, including:
  • GROMACS
  • HMMer
  • LSQRMS
  • MrBayes
• locally-created Perl programs for research
• Files about the proteins I used
• Files for input to programs (put.together.pdbs.*) putting together templates and/or loop search results
• database of species and structures plus info on the local version of the NCBI taxonomy
• structural models, including homology models and locally-minimized experimental structures from the PDB
• phylogenetic trees, of variable reliability, and some analysis
• AO.NO.constraints.ascomycota.txt, on the constraints (as if NMR distance restraints) I used between NADPH and DHFR in minimizations
• DHFR.with.fungi.2.seqs.edited.7.vert.xls - partial version of DHFR alignment - NOT VERY RELIABLE
• DHFR.with.fungi.2.stockholm.txt - current DHFR plus DHFR/TS alignment in Stockholm format - NOT VERY RELIABLE

Page written by Allen Smith (send mail to meatcan2@beatrice.rutgers.edu, substituting easmith for meatcan2 - see my antispam page(s)for why).

I am not responsible for any pages linked from these, except for those that I have written. Neither is the Structural Biology Computational Laboratory, the Department of Biochemistry and Microbiology, Cook College, or Rutgers University responsible for (or have any copyright on) pages that I have written. My webpages are not official Rutgers webpages.

This webpage, and all other files in or under this directory (except for those explicitly copyrighted or licensed otherwise), are licensed (copyright 2001-2008) by Allen Smith under a Creative Commons Attribution-ShareAlike 2.5 License; also see legalcode.txt for a text version of the Legal Code of the license. (Of course, factual material is not copyrightable - fortunately!)