Simulation in Chemistry & Biochemistry

Chemistry 430

Spring Term 2021

Coursemaster: Jay Ponder


General Information

Syllabus & Schedule [PDF]

Zoom Link for Class Sessions [LINK]


LECTURE SUMMARIES

Lecture 1 (Jan 25): Overview of Molecular Modeling [PDF] [MP4]

Lecture 2 (Jan 27): Introduction to Molecular Mechanics I [PDF] [MP4]

Lecture 3 (Feb 01): Introduction to Molecular Mechanics II [MP4]

Lecture 4 (Feb 03): Potential Energy Surfaces & Optimization Methods [PDF] [MP4]

Lecture 5 (Feb 08): Basics of Molecular Dynamics Simulation I [PDF] [MP4]

Lecture 6 (Feb 10): Basics of Molecular Dynamics Simulation II [MP4]

Lecture 7 (Feb 15): Computing Properties from Molecular Dynamics I [PDF] [MP4]

Lecture 8 (Feb 17): Computing Properties from Molecular Dynamics II [MP4]

Lecture 9 (Feb 22): Introduction to Monte Carlo Methods I [PDF] [MP4]

Lecture 10 (Feb 24): Introduction to Monte Carlo Methods II [MP4]

Lecture 11 (Mar 01): Methods for Free Energy Calculations [PDF] [MP4]

Lecture 12 (Mar 03): Proteins I: Amino Acids & Secondary Structure [PDF] [MP4]

Lecture 13 (Mar 08): Proteins II: Tertiary Structure, Motifs & Fold Classes [PDF] [MP4]

Lecture 14 (Mar 10): Proteins III: Mechanism of Protein Folding [PDF] [MP4]

Lecture 15 (Mar 15): Electrostatics & Solvation in Biomolecular Systems I [PDF] [MP4]

Lecture 16 (Mar 17): Electrostatics & Solvation in Biomolecular Systems II [MP4]

Lecture 17 (Mar 22): Basics of ab Initio Molecular Orbital Theory I [PDF] [MP4]

Lecture 18 (Mar 24): Basics of ab Initio Molecular Orbital Theory II [MP4]

Lecture 19 (Mar 29): Methods for Treating Electron Correlation [PDF] [MP4]

Lecture 20 (Mar 31): Semi-Empirical Molecular Orbital Methods [PDF] [MP4]

Lecture 21 (Apr 05): Density Functional Theory I [PDF] [MP4]

Lecture 22 (Apr 07): Density Functional Theory II [MP4]

Lecture 23 (Apr 12): QM/MM Methods; Frontier Orbital Theory [PDF]

Lecture 24 (Apr 14): Protein Structure Prediction, Engineering & Design [PDF] [MP4]

Lecture 25 (Apr 19): Small Molecule & Protein Docking I [PDF] [MP4]

Lecture 26 (Apr 21): Small Molecule & Protein Docking II [MP4]

Lecture 27 (Apr 26): Computing Binding Rate Constants via Brownian Dynamics [PDF] [MP4]

Lecture 28 (Apr 28): Introduction to Convolutional Neural Networks [PDF] [MP4]

Lecture 29 (May 03): Machine Learning in Computational Chemistry [PDF] [MP4]


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]

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]

The RHF Dissociation Problem, Section 4.3 from Introduction
to Computational Chemistry, 2nd Edition, by F. Jensen,
John Wiley & Sons, Chichester UK, 2007 [PDF]

The Difference Between Configuration Interaction & Coupled Cluster,
Chemistry Stack Exchange Online, February 2017 [PDF]

Derivation of Moeller-Plesset Perturbation Theory,
Gaussian, Inc., 2015-2018 [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]

Klopman-Salem Equation, taken from the Wikipedia page [PDF]

Role of Frontier Orbitals in Chemical Reactions, K. Fukui,
Science, 218, 747-754 (1982) [Nobel Prize Award Lecture] [PDF]

An Examination of the Nature of Localized Molecular Orbitals and
their Value in Understanding Phenomena that Occur in Organic Chemistry,
J. J. P. Stewart, Journal of Molecular Modeling, 25, 7 (2019) [PDF]

Density Functional Theory

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

An Introduction to Density Functional Theory,
N. M. Harrison, Department of Chemistry, Imperial College, London [PDF]

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

Density Functional Theory (DFT), Hartree-Fock (HF), and
the Self-Consistent Field, P. M. W. Gill,
Encyclopedia of Computational Chemistry, 1, 678-689 (1998) [PDF]

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

Can Orbitals Really Be Observed? [Warning! Philosophy...]

Can Orbitals Really Be Observed in Scanning Tunneling
Microscopy Experiments, B. Q. Pham and M. S. Gordon,
Journal of Physical Chemistry A, 121, 4851-4852 (2017) [PDF]

Are Orbitals Observable?, P. Mulder,
International Journal for Philosophy of Chemistry, 17, 24-35 (2011) [PDF]

Measuring Orbitals: Provocation or Reality?, W. H. E. Schwarz,
Angewandte Chemie International Edition, 45, 1508-1517 (2006) [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]

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]

Software for Molecular Docking: A Review, N. S. Pagadala,,
K. Syed and J. Tuszynski, Biophysical Reviews, 9, 91-102 (2017) [PDF]

Progress in Molecular Docking, J. Fan, A. Fu and L. Zhang,
Quantitative Biology, 7, 83-89 (2019) [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]

AutoDock Vina: Improving the Speed and Accuracy of Docking with a New
Scoring Function, Efficient Optimization, and Multithreading, O. Trott
and A. J. Olson, Journal of Computational Chemistry, 31, 455-461 (2010) [PDF]

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly
Specified Binding Site Flexibility, P. A. Ravindranath, S. Forli,
D. S. Goodsell, A. J. Olson and M. F. Sanner,
PLoS Computational Biology, 11, e1004586 (2015) [PDF]

Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms
Better Binding Affinity, N. T. Nguyen, T. H. nguyen, T. N. H. Pham,
N. T. Huy, M. V. Bay, M. Q. Pham, P. C. Nam, V. V. Vu and S. T. Ngo,
Journal of Chemical Information and Modeling, 60, 204-211 (2020) [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]

Brownian Dynamics Simulations of Biological Molecules,
G. A. Huber and J. A. McCammon, Trends in Chemistry, 1, 727-738 (2019) [PDF]

Convolutional Neural Networks

Simple Introduction to Convolutional Neural Networks,
M. Stewart, Towards Data Science, February 2019 [PDF]

Basic Introduction to Convolutional Neural Network,
H. S. Chatterjee, Towards Data Science, July 2019 [PDF]

A Quick Introduction to Neural Networks,
U. J. J. Walkarn, The Data Science Blog, August 2016 [PDF]

An Intuitive Explanation of Convolutional Neural Networks,
U. J. J. Walkarn, The Data Science Blog, August 2016 [PDF]

Applications of Neural Networks

Fast and Accurate Modeling of Molecular Atomization Energies
with Machine Learning, M. Rupp, A. Tkatchenko, K.-R. Muller
and O. A. von Lilienfeld, Physical Review Letters, 108, 058301 (2012) [PDF]

Bypassing the Kohn-Sham Equations with Machine Learning,
F. Brockherde, L. Vogt, L. Li, M. E. Tuckerman, K. Burke
and K.-R. Muller, Nature Communications, 8, 872 (2017) [PDF]

ANI-1: An Extensible Neural Network Potential with DFT Accuracy
at Force Field Computational Cost, J. S. Smith, O. Isayev
and A. E. Roitberg, Chemical Science, 8, 3192-3203 (2017) [PDF]

SchNet - A Deep Learning Architecture for Molecular and Materials,
K. T. Schutt, H. E. Sauceda, P.-J. Kindermans, A. Tkatchenko
and K.-R. Muller, Journal of Chemical Physics, 148, 241722 (2018) [PDF]

Improved Protein Structure Prediction Using Potentials from Deep Learning,
A. W. Senior, R. Evans, J. Jumper, J. Kirkpatrick, L. Sifre, T. Green,
C. Qin, A. Zidek, A. W. R. Nelson, A. Bridgland, H. Penedones, S. Petersen,
K. Simonyan, S. Crossan, P. Kohl, D. T. Jones, D. Silver, K. Kavukcuoglu
and D. Hassabis, Nature, 577, 706-710 (2020) [PDF]

News in Focus - "It Will Change Everything": AI Makes
Gigantic Leap in Solving Protein Structures, E. Callaway,
Nature, 588, 203-204 (2020) [PDF]

CASP14: What Google DeepMind's AlphaFold2 Really Achieved,
and What It Means for Protein Folding, Biology and Bioinformatics,
C. O. Rubiera, Oxford Protein Informatics Group, December 2020 [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 1.15 Software for macOS [DMG]

Chimera 1.15 Software for Windows [EXE]

Chimera 1.15 Software for Linux [BIN]

Chimera Quick Reference [PDF]

Chimera Getting Started [HTTP]

Chimera User's Guide [HTTP]

ChimeraX: Next-Generation of Chimera Software

ChimeraX 1.1 Software for macOS [DMG]

ChimeraX 1.1 Software for Windows [EXE]

ChimeraX 1.1 Software for Ubuntu Linux [DEB]

ChimeraX 1.1 Software for RedHat Linux [RPM]

ChimeraX 1.1 Software for Generic Linux [GZIPPED TAR]]

ChimeraX Overview [PDF]

ChimeraX Features [PDF]

ChimeraX Tutorial [PDF]

ChimeraX Publication [PDF]

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 (10.10 thru 10.13) [DMG]

VMD 1.9.4 Software for macOS (10.15, Catalina) [DMG]

VMD 1.9.4 Software for macOS (11, Big Sur, Intel) [DMG]

VMD 1.9.4 Software for macOS (11, Big Sur, Apple M1) [DMG]

VMD 1.9.4 Software for Windows [EXE]

VMD 1.9.4 Software for Linux [GZIPPED TAR]

VMD User's Guide [PDF]

Using VMD Tutorial [PDF]

VMD Tutorial Files [GZIPPED TAR]

Spartan Student Molecular Modeling

Spartan Student V6 Software for macOS [DMG]

Spartan Student V6 Software for Windows [EXE]

Spartan Student V7 Software for macOS [DMG]

Spartan Student V7 Software for Windows [EXE]

Spartan Student V8 Software for macOS [DMG]

Spartan Student V8 Software for Windows [EXE]

Spartan Student Overview [PDF]

Spartan Student Tutorial [PDF]

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

Spartan '14 Manual [PDF]

Tinker: Software Tools for Molecular Design

Tinker 8.8.3 Software for macOS [GZIPPED TAR]

Tinker 8.8.3 Software for Windows [ZIP]

Tinker 8.8.3 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]

Using PDB2PQR Documentation [HTML]

Using APBS Documentation [HTML]

Gaussian Quantum Chemistry

Gaussian 16 Online Manual [HTML]

GaussView 6 Online Manual [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]

AutoDock4 & MGLTools: Automated Molecular Docking

AutoDock 4.2.6 Software for macOS [TAR]

AutoDock 4.2.6 Software for Windows [ZIP]

AutoDock 4.2.6 Software for Linux [TAR]

AutoDock 4.2.6 Installation for Linux & macOS [PDF]

AutoDock 4.2.6 Installation for Windows [PDF]

AutoDock 4.2.6 User's Guide [PDF]

MGLTools 1.5.7 Software for macOS (10.14 & earlier only!) [DMG]

MGLTools 1.5.7 Software for Windows [ZIP]

MGLTools 1.5.7 Software for Linux [SCRIPT]

XQuartz 2.7.11 for MacOS (needed by MGLTools on Mac) [DMG]

Tutorial: Docking Indinavir to HIV Protease [PDF]

Tutorial: Docking of BACE1 with an Inhibitor [PDF]

SDA7: Simulation of Diffusional Association

SDA7 Documentation [HTML]


LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 29): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]

Lab 2 (Feb 05): Conformational Analysis of Alanine Dipeptide [Files]

Lab 3 (Feb 12): Liquid Properties via Molecular Dynamics Simulation [Files]

Lab 4 (Feb 19): Global Optimization of Lennard-Jonesium & Polyalanine [Files]

Lab 5 (Feb 26): Relative Hydration Free Energy of Monovalent Ions [Files]

Lab 6 (Mar 05): Folding Simulations of the TrpCage MiniProtein [Files]

Lab 7 (Mar 19): APBS Poisson-Boltzmann Calculations on Lysozyme [Files]

Lab 8 (Apr 02): Computing the Rotational Barrier in Hydrazine [Files]

Lab 9 (Apr 09): Frontier Molecular Orbital Analysis of Regioselectivity [Files]

Lab 10 (Apr 16): Homology Modeling of a Lactate Dehydrogenase [Files]

Lab 11 (Apr 23): Docking Indinavir to HIV Protease Using AutoDock [Files]

Lab 12 (Apr 30): Diffusional Association of the Barnase-Barstar Complex [Files]