SIMULATION IN CHEMISTRY & BIOCHEMISTRY

Chemistry 430

Spring Term 2020

Instructor: Jay Ponder


GENERAL INFORMATION

Syllabus & Schedule [PDF]


LECTURE SUMMARIES

Lecture 1 (Jan 13): Overview of Molecular Modeling [PDF]

Lecture 2 (Jan 15): Introduction to Molecular Mechanics I [PDF]

Lecture 3 (Jan 22): Introduction to Molecular Mechanics II

Lecture 4 (Jan 27): Potential Energy Surfaces & Optimization Methods [PDF]

Lecture 5 (Jan 29): Basics of Molecular Dynamics Simulation I [PDF]

Lecture 6 (Feb 03): Basics of Molecular Dynamics Simulation II

Lecture 7 (Feb 05): Computing Properties from Molecular Dynamics [PDF]

Lecture 8 (Feb 10): Introdution to Monte Carlo Methods I [PDF]

Lecture 9 (Feb 12): Introdution to Monte Carlo Methods II

Lecture 10 (Feb 17): Methods for Free Energy Calculations [PDF]

Lecture 11 (Feb 19): Electrostatics & Solvation in Biomolecular Systems I [PDF]

Lecture 12 (Feb 24): Electrostatics & Solvation in Biomolecular Systems II

Lecture 13 (Feb 26): Proteins I: Amino Acids & Secondary Structure [PDF]

Lecture 14 (Mar 02): Proteins II: Tertiary Structure, Motifs & Fold Classes [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]

Biomolecular Force Fields: Where Have We Been, Where Are We Now,,
Where Do We Need To Go and How Do We Get There?, P. Dauber-Osguthorpe
and A. T. Hagler, Journal of Computer-Aided Molecular Design, 33, 133-203 (2019) [PDF]

Force Field Development Phase II: Relaxation of Physics-Based
Criteria... or Inclusion of More Rigorous Physcs Into the Representation
of Molecular Physics, A. T. Hagler, Journal of Computer-Aided Molecular
Design, 33, 205-264 (2019) [PDF]

Nonlinear Optimization Methods

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

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

Molecular Dynamics Simulation

Simulation Methods & Molecular Dynamics, Chapter 6 & 7 from Molecular
Modelling: Principles & Applications, 2nd Edition by A. R. Leach, [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

Monte Carlo Simulation Methods, Chapter 8 from Molecular Modelling:
Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

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, Chapter 11 from Molecular Modelling:
Principles & Applications, 2nd Edition by A. R. Leach, [PDF]

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]

Accurate Calculation of the Absolute Free Energy of Binding for Drug
Molecules, M. Aldeghi, A. Heifetz, M. J. Bodkin, S. Knapp and P. C. Biggin,
Chemical Science, 7, 207-218 (2016) [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]

Comparative & Homology Modeling

Protein Structure Modeling with MODELLER, B. Webb and A. Sali,
Methods in Molecular Biology, 1654, 39-54 (2017) [PDF]

SWISS-MODEL: Homology Modelling of Protein Structures and Complexes,
A. Waterhouse, M. Bertoni, S. Beinert, G. Studer, G. Tauriello, R. Gumienny,
F. T. Heer, T. A. P. de Beer, C. Rempfer, L. Bordoli, R. Lepore and T. Schwede,
Nucleic Acids Research, 46, W296-303 (2018) [PDF]

The Phyre2 Web Portal for Protein Modeling, Prediction and Analysis,
L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass and M. J. E. Sternberg,
Nature Protocols, 10, 845-858 (2015) [PDF]


SOFTWARE RESOURCES

General Information

How to Install Non-AppStore Programs on MacOS [PDF]

How to Disable the (Annoying!) Gatekeeper on MacOS [PDF]

Avogadro & Avogadro2: Molecular Editors

Avogadro 1.2.0 Software for MacOS [DMG]

Avogadro 1.2.0 Software for Windows [EXE]

Avogadro2 1.91 Software for MacOS [DMG]

Avogadro2 1.91 Software for Windows [EXE]

Learning Avogadro [PDF]

Avogadro Example Files [GZIPPED TAR]

Chimera: Extensible Molecular Modeling System

Chimera 1.13 Software for MacOS [DMG]

Chimera 1.13 Software for Windows [EXE]

Chimera 1.13 Software for Linux [BIN]

Chimera Quick Reference [PDF]

Chimera Getting Started [HTTP]

Chimera User's Guide [HTTP]

PyMOL: Python-Enhanced Molecular Graphics

PyMOL 1.7.4.5 Software for MacOS [DMG]

PyMOL 1.7.4.5 Software for Windows [MSI]

PyMOL 1.7.4.5 Software for Linux [GZIPPED TAR]

PyMOL Quick Reference [PDF]

PyMOL Introduction [PDF]

PyMOL Tutorial [PDF]

PyMOL User's Guide [PDF]

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]

Tinker: Software Tools for Molecular Design

Tinker 8.7.2 Software for MacOS [GZIPPED TAR]

Tinker 8.7.2 Software for Windows [ZIP]

Tinker 8.7.2 Software for Linux [GZIPPED TAR]

Tinker Manual [PDF]

FFE: Force Field Explorer

Force Field Explorer 8.7.2 Software for MacOS [DMG]

Force Field Explorer 8.7.2 Software for Windows [ZIP]

Force Field Explorer 8.7.2 Software for Linux [GZIPPED SH]

Force Field Explorer Manual [PDF]

APBS: Adaptive Poisson-Boltzmann Solver

APBS 1.3 Software for MacOS [GZIPPED TAR]

APBS 1.3 Software for Windows [ZIP]

APBS 1.3 Software for Linux [GZIPPED TAR]

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]

Modeller: Comparative Protein Structure Modeling

Modeller 9.21 Software for MacOS [DMG]

Modeller 9.21 Software for Windows [ZIP]

Modeller 9.21 Software for Linux (Ubuntu & Debian) [DEB]

Modeller 9.21 Software for Linux (RedHat & CentOS) [RPM]

Modeller 9.21 Installation Instructions [PDF]

Modeller 9.21 Manual [PDF]

Chimera Interface to Modeller [PDF]

Tutorial: Modeling Based on a Single Template [PDF] Files [GZIPPED TAR]

Tutorial: Multiple Templates, Loop Refinement & User Restraints [PDF]

Tutorial: The Alignment-Modeling-Evaluation Cycle [PDF]

Tutorial: Modeling a Sequence after Fold Assignment [PDF]

Tutorial: Use of Cryo-EM Data in Modeling [PDF]


LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 17): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]

Lab 2 (Jan 24): Conformational Analysis of Alanine Dipeptide [Files]

Lab 3 (Jan 31): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 4 (Feb 07): Global Optimization of Lennard-Jonesium & Polyalanine [Files]

Lab 5 (Feb 14): Relative Hydration Free Energy of Monovalent Ions [Files]

Lab 6 (Feb 21): APBS Poisson-Boltzmann Calculations on Lysozyme [Files]

Lab 7 (Feb 28): Homology Modeling of a Lactate Dehydrogenase [Files]