SIMULATION IN CHEMISTRY & BIOCHEMISTRY

Chemistry 430

Spring Term 2018

Instructor: Jay Ponder


GENERAL INFORMATION

Syllabus & Schedule [PDF]


LECTURE SUMMARIES

Lecture 1 (Jan 17): Overview of Molecular Modeling [PDF]

Lecture 2 (Jan 22): Introduction to Molecular Mechanics I [PDF]

Lecture 3 (Jan 24): Introduction to Molecular Mechanics II

Lecture 4 (Jan 29): Potential Energy Surfaces & Optimization Methods [PDF]

Lecture 5 (Jan 31): Basics of Molecular Dynamics Simulation I [PDF]

Lecture 7 (Feb 07): Computing Properties from Molecular Dynamics [PDF]

Lecture 8 (Feb 12): Introdution to Monte Carlo Methods I [PDF]

Lecture 9 (Feb 14): Introdution to Monte Carlo Methods II

Lecture 10 (Feb 19): Methods for Free Energy Calculations [PDF]

Lecture 11 (Feb 21): Proteins: Amino Acids & Secondary Structure [PDF]

Lecture 12 (Feb 26): Proteins: Tertiary Structure, Motifs & Fold Classes [PDF]

Lecture 13 (Feb 28): Electrostatics & Solvation in Biomolecular Systems I [PDF]

Lecture 14 (Mar 05): Electrostatics & Solvation in Biomolecular Systems II

Lecture 15 (Mar 07): Proteins: Mechanism of Protein Folding [PDF]

Lecture 16 (Mar 19): Basics of ab Initio Molecular Orbital Theory I [PDF]

Lecture 17 (Mar 21): Basics of ab Initio Molecular Orbital Theory II

Lecture 18 (Mar 26): Methods for Treating Electron Correlation [PDF]

Lecture 19 (Mar 28): Semi-Empirical Molecular Orbital Methods [PDF]

Lecture 20 (Apr 02): Density Functional Theory (DFT) [PDF]

Lecture 21 (Apr 04): Quantum Mechanics/Molecular Mechanics (QM/MM) [PDF]

Lecture 22 (Apr 09): Protein Structure Prediction, Engineering & Design [PDF]

Lecture 23 (Apr 11): Small Molecule & Protein Docking I [PDF]

Lecture 24 (Apr 16): Small Molecule & Protein Docking II

Lecture 25 (Apr 18): Computing Binding Rate Constants via Brownian Dynamics [PDF]


READINGS & REFERENCES

Introduction to Using a Linux Terminal Window

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

Useful Unix/Linux 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]

Molecular Mechanics & Force Fields

Empirical Force Field Models, Chapter 4 from Molecular Modelling:
Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

Nonlinear Optimization Methods

Molecular Modelling: Principles & Applications, 2nd Ed.,
A. R. Leach, Chapter 5: Energy Minimization & Related Methods [PDF]

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

Molecular Dynamics Simulation

Molecular Modelling: Principles & Applications, 2nd Ed.,
A. R. Leach, Chapters 6 & 7: Simulation Methods & Molecular Dynamics [PDF]

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]

Protein Structure & Taxonomy

Molecular Modeling & Simulation: An Interdisciplinary Guide, 2nd Ed.,
T. Schlick, Chapters 3 & 4: Protein Structure Introduction & Hierarchy [PDF]

The Anatomy and Taxonomy of Protein Structure, J. S. Richardson,
[Updated by D. C. Richardson and J. S. Richardson, 2000-2007]
Advances in Protein Chemistry, 34, 167-339 (1981) [PDF]

Interesting Web Sites for Protein Structural Analysis [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

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

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]

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]

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]

Molecular Docking Methods

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]

Molecular Docking and Structure-Based Drug Design Strategies,
L. G. Ferreira, R. N. dos Santos, G. Oliva and A. D. Andricopulo,
Molecules, 20, 13384-13421 (2015) [PDF]

Structure-based Discovery of Opioid Analgesics with Reduced Side Effects,
A. Manglik, H. Lin, D. K. Aryal, J. D. McCorvy, D. Dengler, G. Corder,
A. Levit, R. C. Kling, V. Bernat, H. Hubner, X.-P. Huang, M. F. Sassano,
P. M. Giguere, S. Lober, D. Duan, G. Scherrer, B. K. Kobilka, P. Gmeiner,
B. L. Roth and B. K. Shoichet, Nature, 537, 185-190 (2106) [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]

Brownian Dynamics Simulation

Biological Applications of Electrostatic Calculations
and Brownian Dynamics Simulations, J. D. Madura, M. E. Davis,
M. K. Gilson, R. C. Wade, B. A. Luty and J. A. McCammon,
Reviews in Computational Chemistry, 4, 229-267 (1994) [PDF]

Brownian Dynamics, Molecular Dynamics, and Monte Carlo
Modeling of Colloidal Systems, J. C. Chen and A. S. Kim,
Advances in Colloid and Interface Science, 112, 159-173 (2004) [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]

Neural Networks and Deep Learning

An Intuitive Explanation of Convolutional Neural Networks [HTML]

Deep Learning for Computational Chemistry, G. B. Goh, N. O. Hodas
and A. Vishnu, Journal of Computational Chemistry, 38, xxx-xxx (2017) [PDF]

Big Data Meets Quantum Chemistry Approximations: The Delta-Machine,
R. Ramakrishnan, P. O. Dral, M. Rupp and O. A. von Lileinfeld,
Journal of Chemical Theory and Computation, 11, 2087-2096 (2015) [PDF]

Transferable Atomic Multipole Machine Learning Models for Small,
Organic Molecules, T. Bereau, D. Andrienko and O. A. von Lileinfeld,
Journal of Chemical Theory and Computation, 11, 3225-3233 (2015) [PDF]

Learning Scheme to Predict Atomic Forces and Accelerate Materials Simulations,
V. Botu and R. Ramprasad, Physical Review B, 92, 094306 (2015) [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 1.12 Software for MacOS [DMG]

Chimera 1.12 Software for Windows [EXE]

Chimera 1.12 Software for Linux [BIN]

Chimera Quick Reference [PDF]

Chimera Getting Started [HTTP]

Chimera User's Guide [HTTP]

VMD: Visual Molecular Dynamics

VMD 1.9.4 Software for MacOS [DMG]

VMD 1.9.3 Software for Windows [MSI]

VMD 1.9.4 Software for Linux [GZIPPED TAR]

VMD User's Guide [PDF]

Using VMD Tutorial [PDF]

VMD Tutorial Files [GZIPPED TAR]

FFE: Force Field Explorer

Force Field Explorer 8.2.1 Software for MacOS [DMG]

Force Field Explorer 8.2.1 Software for Windows [ZIP]

Force Field Explorer 8.2.1 Software for Linux [GZIPPED SH]

Force Field Explorer Manual [PDF]

TINKER Software Tools for Molecular Design

TINKER 8.3 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]

pKa Calculations in APBS [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 19): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]

Lab 2 (Jan 26): Conformational Analysis of Alanine Dipeptide [Files]

Lab 3 (Feb 02): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 4 (Feb 09): Global Optimization of Lennard-Jonesium & Polyalanine [Files]

Lab 5 (Feb 16): Relative Hydration Free Energy of Monovalent Ions [Files]

Lab 6 (Feb 23): Normal Modes & Vibrational Spectra of Water, Benzene & Phenol [Files]

Lab 7 (Mar 02): APBS Poisson-Boltzmann Calculations on Lysozyme [Files]

Lab 8, Part 1 (Mar 09): Folding Simulations of the TrpCage MiniProtein [Files]

Lab 9 (Mar 23): Computing the Rotational Barrier in Hydrazine [Files]

Lab 8, Part 2 (Mar 30): Folding Simulations of the TrpCage MiniProtein [Files]

Lab 10 (Apr 06): Frontier Molecular Orbital Analysis of Regioselectivity [Files]

Lab 11 (Apr 13): Docking Indinavir to HIV Protease Using AutoDock [Files]

Lab 12 (Apr 20): Diffusional Association of the Barnase-Barstar Complex [Files]