Molecular Modeling and Simulation: An Interdisciplinary Guide

Tamar Schlick

List of Figures

1 Biomolecular Sructure and Modeling: Historical Perspective
1.1 Simulation evolution (3D version)
1.2 Simulation evolution (2D version)
1.3 Cryo-EM view of - latrotoxin
2 Biomolecular Structure and Modeling: Problem and Application Perspective
2.1 Sequence and Structure Data
2.2 Paracelsus' Janus
2.3 GroEL/GroES chaperonin/co-chaperonin complex
2.4 Prion protein
2.5 AIDS drugs
3 Protein Basic
3.1 An amino acid
3.2 Water clusters
3.3 Dipeptide formation
3.4 Peptide formula
3.5 Aspartame
3.6 The amino acid repertoire
3.7 Amino acids structures
3.8 Amino acid frequencies
3.9 Fibrous proteins
3.10 Rop
3.11 EF Proteins
3.12 Protein-structure variants
3.13 Gauche and trans orientations
3.14 Dihedral angle
3.15 Rotations in polypeptides
3.16 Amino acids rotamers
3.17 Ramachandran plots
3.18 Further Study of Ramachandran plots
4 Protein Hierarchy
4.1 The - helix and - sheet motifs
4.2 - helical proteins (a)
4.3 - helical proteins (b)
4.4 - helical proteins (a)
4.5 - helical proteins (b)
4.6 / proteins
4.7 + proteins
4.8 Tomato bushy stunt virus
5 Nucleic Acids Structure
5.1 The DNA double helix
5.2 Nucleic acid components
5.3 Watson-Crick base pairing
5.4 The polynucleotide chain and labeling
5.5 Sugar envelope and twist puckers
5.6 Sugar pseudorotation cycle
5.7 Common sugar puckers
5.8 Sugar pucker clustering
5.9 Torsion angle wheel
5.10 Deoxyadenosine adiabatic map
5.11 Base-pair coordinate system
5.12 Base-pair step and base pair parameters
5.13 Model A, B, and Z-DNA
5.14 Model A, B, and Z-DNA, stereo side
5.15 Model A, B, and Z-DNA, stereo top
6 Topics in Nucleic Acids Structure
6.1 Bending in long DNA
6.2 Net DNA bending examples
6.3 A-tract DNA dodecamer
6.4 Sequence-dependent local DNA hydration
6.5 DNA/protein binding motifs
6.6 Various hydrogen-bonding schemes
6.7 DNA/protein complex with Hoogsteen bp
6.8 Oligonucleotide analogues
6.9 Various nucleotide-chain folding motifs
6.10 RNAs with pseudoknots
6.11 Interwound and toroidal supercoiling
6.12 Nucleosome core particle
6.13 Schematic view of DNA levels of folding
6.14 Supercoiling topology and geometry
6.15 Brownian dynamics snapshots of DNA
6.16 Site juxtaposition measurements
6.17 Polynucleosome modeling
7 Theoretical Approaches
7.1 DNA quantum-mechanically derived electrostatic potentials
7.2 Enolase active site
7.3 Molecular geometry
7.4 CHARMM Atom types
8 Force Fields
8.1 Normal modes of a water molecule.
8.2 Computed protein and water spectra
8.3 Vibrational modes types
8.4 Bond-length potentials
8.5 Bond angles
8.6 Bond-angle potentials
8.7 Stretch/bend cross terms
8.8 Butane torsional orientations
8.9 Torsion-angle potentials
8.10 Model compounds for torsional parameterization
8.11 Wilson angle
8.12 Van der Waals potentials
8.13 Coulombic potentials
9 Nonbonded Computations
9.1 CPU Time for Nonbonded Calculations
9.2 Cutoff schemes
9.3 Switch and shift functions
9.4 Periodic domains
9.5 Various periodic domains
9.6 Space-filling polyhedra
9.7 Ewald's trick of Gaussian masking
9.8 CPU Time for PME vs. Fast Multipole
9.9 Fast multipole schemes
9.10 Screened Coulomb potential
9.11 Poisson-Boltzmann Rendering of the 30S Ribosome
10 Multivariate Minimization
10.1 One-dimensional function
10.2 2D Contour curves for quadratic functions
10.3 3D curves for quadratic functions
10.4 Sparse Hessians
10.5 Sparse Hessians, continued
10.6 Line search minimization
10.7 Newton's method, simple illustration
10.8 Newton's method, quadratic example output
10.9 Newton's method, cubic example output
10.10 Minimization paths
10.11 Minimization progress
11 Monte Carlo Techniques
11.1 Lattice structure for simple random number generators
11.2 Lattice structure for linear congruential generator
11.3 MC computation of
11.4 Boltzmann probabilities
11.5 MC moves for DNA
11.6 MC and BD DNA Distributions
11.7 Bad MC Protocol
12 Molecular Dynamics: Basics
12.1 Sampling methods
12.2 Equilibration
12.3 Chaos in MD
12.4 Butane's end-to-end distance
12.5 Butane's end-to-end distance convergence
12.6 Energy drift
13 Molecular Dynamics: Further Topics
13.1 Effective Verlet phase space rotation
13.2 Verlet resonance for a Morse oscillator
13.3 Extrapolative vs. Impulse MTS
13.4 Impulse vs. Extrapolative Force Splitting
13.5 Resonance from Force Splitting
13.6 Harmonic Oscillator Langevin Trajectories
13.7 BPTI means and variances by Langevin and Newtonian force splitting
13.8 LN algorithm
13.9 Manhattan plots for polymerase/DNA
13.10 Polymerase/DNA geometry
13.11 BPTI spectral densities
13.12 Polymerase/DNA spectral densities
13.13 Polymerase/DNA geometry
13.14 Cholesky vs. Chebyshev approaches for the BD random force
13.15 Implicit and explicit Euler
13.16 Verlet and implicit-midpoint energies
13.17 Stochastic-path approach snapshots
14 Similarity and Diversity
14.1 Sample drugs
14.2 Related pairs of drugs
14.3 Chemical library
14.4 SVD/refinement performance
14.5 SVD-based database projection in 2D and 3D
14.6 Cluster analysis
14.7 PCA projection in 2D, with similar pairs
14.8 PCA projection in 2D, with diverse pairs
Appendix A Syllabus  (PDF)
Appendix B Article Reading List
Appendix C General Reference List
Appendix D Homeworks
D.1 Sample histogram for protein/DNA interaction analysis
D.2 Biphenyl
D.3 Structure for linear congruential generators
Bibliography
References




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