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This page contains several documents relating to computational chemistry.
Documents are ordered by the date when they were placed in the
CCL archives. Note that CCL archives existed BEFORE the advent of WWW
(initially as FTP and MAILSERV, then GOPHER was added as a retrieval
mechanism). If you have useful material to contribute to this
page, please share and upload it to CCL Archive using
the CCL UPLOAD PAGE.
- 2008.01.10 Protonate 3D:
Assignment of Macromolecular Protonation
State and Geometry by Paul Labute,
Chemical Computing Group.
Protonate 3D is an application which assigns protonation states and geometries
(taking titration into account) to macromolecular structures using an
algorithm that solves the Unary Quadratic Optimization problem.
- 2008.01.10 Ligand Scaffold Replacement
using MOE Pharmacophore Tools by Alain Deschênes
and Elizabeth Sourial, Chemical Computing Group.
We describe a scaffold replacement methodology based upon an
extension of MOE's pharmacophore features. The special Link
pharmacophore features can be used in conjunction with other features, SMARTS
patterns and volume constraints.
- 2007.10.25 STERIMOL Documentation
submitted by Dr. Steve Bowlus.
- 2007.02.12 Homology Modelling
by Dr. Dimitrios P.Vlachakis. As short write-up on the principles
of Homology Modelling.
- 2006.11.09 Vibrational Transition Moments and
Dipole Derivatives -- A write-up by T. Daniel Crawford, Virginia Tech.
Learn the theory behind oscillator strengths and integrated absorption
intensities for vibrational (infrared) spectra.
- 2006.08.28 MMCC Results Newsletter: Literature survey
for molecular modeling and computational chemistry.
- 2006.02.17 Dr. Sengen Sun's paper on "Mechanism of concerted cycloadditions"
and PowerPoint Slides:Mechanism of Concerted
Cycloadditions as a Philosophical Challenge in Chemistry.
- 2005.12.10 Unfinished
paper on proton affinities (ca. 1994). Methodology description,
experimental and computed results. PDF and LaTeX files.
- 2004.04.13 Which Linux to use in a research/educational envioronment?
- 2003.03.10 Computational Chemistry
on 64 bit machines by Daniel Svozil
- 2001.01.03 Computational chemistry topics and visualization
of ab initio results for
water molecule
courtesy of David Young
Dave_Young-at-cytoclonal.com.
- 2000.11.30 Quick Reference Guide
to Computational Chemistry Acronyms,
Methods, Parameters, Accuracy, and Software by Ernie Chamot.
- 1999.04.11 Courseware
-- An overview of the computational chemistry course at the
University of Minnesota
- 1997.10.15 Overview
of some aspects of molecular modeling
- 1997.03.29 High Performance Fortran
-- A description of the High Performance Fortran
standard
- 1996.12.04 Overview of Density
Functional Theory as well as
some notes
on Density Functional Theory software. The
LaTeX source and
PostScript of the Overview is also available (Watch, it is getting
outdated fast!!!).
- 1996.10.03 EHT Bibliography
- 1996.01.15 A Survey of CCL
users in the summer of 1994.
- 1995.08.30 Cartesian to Internal
-- Synpsis of one CCL discussion.
- 1994.03.31 Molecular Graphics Packages in March, 1994.
- 1992.10.07 Mopac 6 manual.
- 1992.04.27 ACS COMP News
-- Old News from the COMP Division of the American Chemical
Society
- 1992.02.03 Drug Designer's Guide
-- A short overview of methods used in Computer-Aided
Drug Design.
- 1991.12.12 Protein Data Bank
-- Format of Protein Data Bank structure file and lists of
available structures in the Protein Data Bank
- 1991.12.10 C vs. FORTRAN
-- Transcript of a discussion from the Computational Chemistry
Mailing List about the pros and cons of using C or FORTRAN for
computational chemistry programs
- 1991.04.19 Basis Sets -- Overview of basis sets used in
ab initio quantum calculations
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