SIMULATION IN CHEMISTRY & BIOCHEMISTRY

Chemistry 430

Spring Term 2017

Instructor: Jay Ponder


GENERAL INFORMATION

Syllabus & Schedule [PDF]


LECTURE SUMMARIES

Lecture 1 (Jan 18): Overview of Molecular Modeling [PDF]

Lecture 2 (Jan 23): Introduction to Molecular Mechanics I [PDF]

Lecture 3 (Jan 25): Introduction to Molecular Mechanics II

Lecture 4 (Jan 30): Potential Energy Surfaces & Optimization Methods [PDF]

Lecture 5 (Feb 01): Basics of Molecular Dynamics Simulation I [PDF]

Lecture 6 (Feb 06): Basics of Molecular Dynamics Simulation II

Lecture 7 (Feb 08): Using Molecular Dynamics to Compute Properties [PDF]

Lecture 8 (Feb 13): Introduction to Monte Carlo Methods I [PDF]

Lecture 9 (Feb 15): Introduction to Monte Carlo Methods II

Lecture 10 (Feb 20): Methods for Free Energy Calculations [PDF]

Lecture 11 (Feb 22): Proteins: Amino Acids & Secondary Structure [PDF]

Lecture 12 (Feb 27): Proteins: Tertiary Structure, Motifs & Fold Classes [PDF]

Lecture 13 (Mar 01): Proteins: Mechanism of Protein Folding [PDF]

Lecture 14 (Mar 06): Electrostatics & Solvation in Biomolecular Systems I [PDF]

Lecture 15 (Mar 08): Electrostatics & Solvation in Biomolecular Systems II

Lecture 16 (Mar 20): Basics of ab Initio Molecular Orbital Theory I [PDF]

Lecture 17 (Mar 22): Basics of ab Initio Molecular Orbital Theory II

Lecture 18 (Mar 27): Methods for Treating Electron Correlation [PDF]

Lecture 19 (Mar 29): Semi-Empirical Molecular Orbital Methods [PDF]

Lecture 20 (Apr 03): Density Functional Theory (DFT) [PDF]

Lecture 21 (Apr 05): Quantum Mechanics/Molecular Mechanics (QM/MM) [PDF]

Lecture 22 (Apr 10): Protein Structure Prediction, Engineering & Design [PDF]

Lecture 23 (Apr 12): Small Molecule & Protein Docking [PDF]

Lecture 24 (Apr 17): Computing Binding Rate Constants via Brownian Dynamics [PDF]

Lecture 25 (Apr 19): Coarse Grained Molecular Modeling [PDF]

Lecture 26 (Apr 24): Structure Determination via Distance Geometry [PDF]

Lecture 27 (Apr 26): Machine Learning in Computational Chemistry

Lecture 28 (Apr 28): Experimental Design Using Multivariate Data Analysis [PDF]


READINGS & REFERENCES

Introduction to Using a Terminal Window (Unix/Linux)

Unix for the Beginning Mage, J. Topjian [PDF]

Useful Unix Tools [HTML]

Perspectives on Molecular Modeling

Biomolecular Modeling: Goals, Problems, Perspectives,
W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen,
X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger, M. A. Kastenholz,
C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt and H. B. Yu,
Angewandte Chemie International Edition, 45, 4064-4092 (2006) [PDF]

Biomolecular Modeling and Simulation: A Field Coming of Age,
T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung and X. Xiao,
Quarterly Reviews of Biophysics, 44, 191-228 (2011) [PDF]

Nonlinear Optimization Methods

Optimization Methods in Computational Chemistry, T. Schlick,
Reviews in Computational Chemistry, 3, 1-71 (1992) [PDF]

Molecular Dynamics Simulation

Molecular Dynamics, J. Meller,
Encyclopedia of Life Sciences, 1-8 (2001) [PDF]

Introduction to Molecular Dynamics Simulation, M. P. Allen,
Computational Soft Matter, NIC Series, 23, 1-28 (2004) [PDF]

Molecular Dynamics: Survey of Methods for Simulating
the Activity of Proteins, S. A. Adcock and J. A. McCammon,
Chemical Reviews, 106, 1589-1615 (2006) [PDF]

History of the Monte Carlo Method

Equation of State Calculations by Fast Computing Machines, N. Metropolis,
A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller and E. Teller,
Journal of Chemical Physics, 21, 1087-1092 (1953) [PDF]

Perspectives on "Equation of State Calculations by Fast Computing
Machines", W. L. Jorgensen, Theoretical Chemistry Accounts,
103, 225-227 (2000) [PDF]

The Beginning of the Monte Carlo Method,
N. Metropolis, Los Alamos Science, 14, 125-130 (1987) [PDF]

Scientific Uses of the MANIAC, H. L. Anderson,
Journal of Statistical Physics, 43, 731-748 (1986) [PDF]

Monte Carlo Theory and Algorithms

Progress and Outlook in Monte Carlo Simulations, D. N. Theodorou,
Industrial & Engineering Chemistry Research, 49, 3047-3058 (2010) [PDF]

Monte Carlo Simulations, D. J. Earl and M. W. Deem,
Methods in Molecular Biology, 443, 25-36 (2008) [PDF]

Monte Carlo Codes, Tools and Algorithms, D. Dubbledam, A. Torres-Knoop
and K. S. Walton, Molecular Simulation, 39, 1253-1292 (2013) [PDF]

Free Energy Calculations

Free Energy Calculations in Structure-Based Drug Design, M. R. Shirts,
D. L. Mobley and S. P. Brown, Chapter 5 from Drug Design: Structure- and
Ligand-Based Approaches, by K. M. Merz Jr., D. Ringe and C. H. Reynolds [PDF]

Towards Accurate Free Energy Calculations in Ligand
Protein-Binding Studies, T. Steinbrecher and A. Labahn,
Current Medicinal Chemistry, 17, 767-785 (2010) [PDF]

Efficient Estimation of Free Energy Differences from Monte Carlo Data,
C. H. Bennett, Journal of Computational Physics, 22, 245-268 (1976) [PDF]

Biomolecular Electrostatics and Solvation

Poisson's Equation in Electrostatics, J.-L. Liu, March 2011 [PDF]

Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics,
W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson,
Journal of the American Chemical Society, 112, 6127-6129 (1990) [PDF]

Computational Methods for Biomolecular Electrostatics, F. Dong,
B. Olsen and N. A. Baker, Methods in Cell Biology, 84, 843-870 (2008) [PDF]

Biomolecular Electrostatics and Solvation: A Computational Perspective,
P. Ren, J. Chun, D. G. Thomas, M. J. Schnieders, M. Marcho, J. Zhang
and N. A. Baker, Quarterly Reviews of Biophysics, 45, 427-491 (2012) [PDF]

Classical Electrostatics for Biomolecular Simulations, G. A. Cisneros,
M. Karttunen, P. Ren and C. Sagui, Chemical Reviews, 114, 779-814 (2014) [PDF]

ab Initio Molecular Orbital Theory

Proof of the Variational Theorem, Appendix B from
Introduction to Computational Chemistry, 2nd Edition, by F. Jensen
John Wiley & Sons, Chichester UK, 2007 [PDF]

Derivation of the Hartree-Fock Equation, Appendix 7 from
Quantum Chemistry, 3rd Edition, by J. P. Lowe and K. A. Peterson
Elsevier Academic Press, Amsterdam, 2006 [PDF]

Computational Quantum Mechanics & Advanced ab Initio Methods,
Chapters 2 & 3 from Molecular Modeling, 2nd Edition by A. R. Leach [PDF]

Density Functional Theory

Perspective: Fifty Years of Density-Functional Theory
in Chemical Physics, A. D. Becke
Journal of Chemical Physics, 140, 18A301 (2014) [PDF]

DFT in a Nutshell, K. Burke and L. O. Wagner
International Journal of Quantum Chemistry, 113, 96-101 (2013) [PDF]

Obituary: Density Functional Theory (1927-1993), P. M. W. Gill
Australian Journal of Chemistry, 54, 661-662 (2001) [PDF]

Approximate Molecular Orbital Methods

The Extended Huckel Method, Chapter 10
from Quantum Chemistry, 3rd Edition by J. P. Lowe and K. A. Peterson [PDF]

Basic Theory of the FMO Method, Chapters 2 & 3
from Frontier Orbitals, by N. T. Anh [PDF]

Molecular Docking Methods

A Critical Assessment of Docking Programs and Scoring Functions,
G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde,
M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger,
G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff and M. S. Head,
Journal of Medicinal Chemistry, 49, 5912-5931 (2006) [PDF]

Challenges and Advances in Computational Docking: 2009 in Review, E. Yurlev,
M. Agostino and P. A. Ramsland, Journal of Molecular Recognition, 24, 149-164 (2011) [PDF]

Protein-Ligand Docking in the New Millennium - A Retrospective of 10
Years in the Field, S. F. Sousa, A. J. M Ribeiro, J. T. S. Coimbra,
R. P. P. Neves, S. A. Martins, N. S. H. N. Moorthy, P. A. Fernandes and
M. J. Ramos, Current Medicinal Chemistry, 20, 2296-2314 (2013) [PDF]

A Review on Molecular Docking: Novel Tool for Drug Discovery,
K. K. Chaudhary and N. Mishra, JSM Chemistry, 4, 1029 (2016) [PDF]

AutoDock Search and Scoring Methodology

Automated Docking Using a Lamarckian Genetic Algorithm and an
Empirical Binding Free Energy Function, G. M. Morris, D. S. Goodsell,
R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew and A. J. Olsen,
Journal of Computational Chemistry, 19, 1639-1662 (1998) [PDF]

A Semiempirical Free Energy Force Field with Charge-Based Desolvation,
R. Huey, G. M. Morris, A. J. Olsen and D. S. Goodsell,
Journal of Computational Chemistry, 28, 1145-1152 (2007) [PDF]

Coarse Grained Modeling with Martini

The MARTINI Force Field: Coarse Grained Model for Biomolecular
Simulations, S.-J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman and
A. H. de Vries, Journal of Physical Chemistry B, 111, 7812-7824 (2007) [PDF]

The Martini Coarse-Grained Force Field, X. Periole and S.-J. Marrink
Methods in Molecular Biology, 924, 533-565 (2013) [PDF]

Perspective on the Martini Model, S.-J. Marrink and D. P. Tieleman
Chemical Society Reviews, 42, 6801-6822 (2013) [PDF]


SOFTWARE RESOURCES

Avogadro Molecular Editor

Avogadro 1.2.0 Software for MacOS [DMG]

Avogadro 1.2.0 Software for Windows [EXE]

Avogadro2 1.90.0 Software for MacOS [DMG]

Avogadro2 1.90.0 Software for Windows [EXE]

Learning Avogadro [PDF}

Avogadro Example Files [GZIPPED TAR}

Chimera: Extensible Molecular Modeling System

Chimera 1.11.2 Software for MacOS [DMG]

Chimera 1.11.2 Software for Windows [EXE]

Chimera Quick Reference [PDF]

Chimera Getting Started [HTTP]

Chimera User's Guide [HTTP]

VMD: Visual Molecular Dynamics

VMD 1.9.3 Software for MacOS [DMG]

VMD 1.9.3 Software for Windows [MSI]

VMD 1.9.3 User's Guide [PDF]

Using VMD Tutorial [PDF]

VMD Tutorial Files [GZIPPED TAR]

FFE: Force Field Explorer

Force Field Explorer 8.0 Software for MacOS [DMG}

Force Field Explorer 7.1 Software for Windows [ZIP}

Force Field Explorer Manual [PDF}

TINKER Software Tools for Molecular Design

TINKER 8.1 Software for MacOS [GZIPPED TAR]

TINKER Manual [PDF}

Spartan Molecular Modeling (Q-Chem)

Spartan Student Overview [PDF]

Spartan Student Tutorial [PDF]

Walking Through Spartan Student (input file for tutorial) [Input]

Spartan '14 Manual [PDF]

Q-Chem 4.1 Manual [PDF]

Gaussian Quantum Chemistry

Gaussian 09 Online Manual [HTML]

GaussView 5 Online Manual [HTML]

APBS Poisson-Boltzmann Solver

PDB2PQR Command Line Usage [HTML]

APBS Command Line Usage [HTML]

APBS Input Files & Options [HTML]

Tutorial: APBS, PDB2PQR, PyMol and VMD [HTML]

Tutorial: Lysozyme pKa Example for PDB2PQR [HTML]

SDA7 (Simulation of Diffusional Association, V7)

SDA7 Documentation [HTML]


LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 20): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]

Lab 2 (Jan 27): Conformational Analysis of Alanine Dipeptide [Files]

Lab 3 (Feb 03): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 4 (Feb 10): Global Optimization of Lennard-Jonesium & PolyAlanine [Files]

Lab 5 (Feb 17): Relative Hydration Free Energy of Monovalent Ions [Files]

Lab 6 (Feb 24): Normal Modes & Vibrational Spectra of Water, Benzene & Phenol [Files]

Lab 7 (Mar 03): APBS Poisson-Boltzmann Calculations on Lysozyme [Files]

Lab 8 (Mar 10): Folding Simulations of the TrpCage MiniProtein [Files]

Lab 9 (Mar 24): Computing the Rotational Barrier in Hydrazine [Files]

Lab 10 (Mar 31): Frontier Molecular Orbital Analysis of Regioselectivity [Files]

Lab 11 (Apr 14): Docking Indinavir to HIV Protease Using AutoDock [Files]

Lab 12 (Apr 21): Diffusional Association of the Barnase-Barstar Complex [Files]