This document contains a set of indexes to the master reference list document. Please note that only the first author is given in the indexes, but complete information can be found by clicking on the reference number.

Broad Molecular Modeling Topics

 Search Medline on molecular modeling (in the last month) or go to the Medline WWW server to perform other kinds of searches.
  1. Computers and Chemistry
  2. "Reviews in Computational Chemistry" (D.B. Boyd)
  3. The Journal of Computational Chemistry

Stereochemistry

Broad Topics

  1. "Introduction to Stereochemistry" (K. Mislow)
  2. "Organic Chemistry", pp. 123-163 (R.T. Morrison)

Model Building

Software

  1. RINGS - A General Program to Build Ring Systems (C.W. vd Lieth)

Databases

  1. "Protein Data Bank Quarterly Newsletter"
  2. The NCI Drug Information System 3D Database (G.W.A. Milne)

Computation Engines

Quantum Chemistry

Broad Topics

  1. "Modern Quantum Chemistry" (A. Szabo)
  2. "Quantum Chemistry" (J.P. Lowe)

Software

  1. "Exploring Chemistry with Electronic Structure Methods: A Guide to Using Gaussian" (J.B. Foresman)

Methods

  1. Semiempirical Molecular Orbital Methods (J.P. Stewart)
  2. Semiempirical Molecular Orbital Methods (M.C. Zerner)

Applications

  1. Ab initio Studies of Structural Features Not Easily Amenable to Experiment (V.J. Klimkowski)

See also UniChem references at Cray Research

Molecular Mechanics

Software
  1. AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions (P.K. Weiner)
  2. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations (B.R. Brooks)
    See also CHARMM references at Molecular Simulations, Inc.
  3. MacroModel - An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics (F. Mohamadi)
  4. Parallelization of CHARMM for MIMD Machines (B.R. Brooks)

Force Fields

  1. A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins (S.J. Weiner)
  2. New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation (P.J. Steinbach)
  3. Validation of the General Purpose Tripos 5.2 Force Field (M. Clark)

Other

  1. "Partition Coefficient, Determination and Estimation" (W.J. Dunn III)

Geometry Engines

Conformational Searching

Rings

  1. Application of the Distance Geometry Algorithm to Cyclic Oligopeptide Conformation Searches (C.E. Peishoff)
  2. Conformations of Cycloheptadecane. A Comparison of Methods for Conformational Searching (M. Saunders)
  3. Different Approaches to Conformational Analysis: A Comparison of Completeness, Efficiency, and Reliability Based on the Study of a Nine-Membered Lactam (H. Bohm)
  4. Pseudorotation: A Large Amplitude Molecular Motion (H.L. Strauss)

Distance Geometry

  1. Application of the Distance Geometry Algorithm to Cyclic Oligopeptide Conformation Searches (C.E. Peishoff)
  2. Conformational Analysis by Energy Embedding (G.M Crippen)

Molecular Dynamics

See also under Biopolymers

Graphics Engines

Broad Topics

  1. The Journal of Molecular Graphics

Software

  1. RasMol: A Program for Fast Realistic Rendering of Molecular Structures With Shadows (R. Sayle)
  2. Raster3D Version 2.0: A Program for Photorealistic Molecular Graphics (E.A. Merritt)

Structure-Activity Relationship Analysis and Drug Design

Broad Topics

  1. "Annual Reports in Medicinal Chemistry" (J.A. Bristol)
  2. "A Textbook of Drug Design and Development" (P. Krogsgaard)
  3. Journal of Medicinal Chemistry
  4. The Journal of Computer-Aided Molecular Design
  5. "Molecular Design and Modeling: Concepts and Applications. Part B: Antibodies and Antigens, Nucleic Acids, Polysaccharides, and Drugs" (J.J. Langone)

Applications

Enzyme Inhibitors

  1. Molecular Modeling Studies of Aldose Reductase Inhibitors (Y.S. Lee)

Biopolymers

Proteins

Broad Topics

  1. "Enzyme Structure and Mechanism" (A. Fersht)
  2. "Introduction to Protein Structure" (C. Branden)
  3. Nature Structural Biology
  4. Protein Engineering
  5. "Proteins" (T.E. Creighton)
  6. Protein Science
  7. "Protein Structure" (M. Perutz)
  8. Proteins: Structure, Function, and Genetics

Molecular Dynamics of Proteins

  1. A Study of Simulated Annealing Protocols for Use with Molecular Dynamics in Protein Structure Prediction (C.A. Laughton)
  2. Computer Modelling of Enzyme Catalyzed Reaction Mechanisms (A.J. Mulholland)
  3. Protein Modeling of Human Prorenin Using the Molecular Dynamics Method (Y. Shiratori)
  4. The Energy Landscapes and Motions of Proteins (H. Frauenfelder)
  5. Theoretical Studies of Relaxation of a Monomeric Subunit of HIV-1 Protease in Water Using Molecular Dynamics (R.M. Venable)

Protein Structure modeling (homology, design, folding)

  1. A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure (J.U. Bowie)
  2. Common Features of the Conformations of Antigen-Binding Loops in Immunoglobulins and Application to Modeling Loop Conformations (A. Tramontano)
  3. Geometry of Proline-Containing Alpha-Helices in Proteins (R. Sankararamakrishnan)
  4. Homology Model of Thyroxine Biding Globulin and Elucidation of the Thyroid Hormone Binding Site (J.A. Jarvis)
  5. Intrahelical Hydrogen Bonding of Serine, Threonine, and Cysteine Residues Within Alpha-Helices and its Relevance to Membrane-bound Proteins (T.M. Gray)
  6. Model Structure for the Human Blood Coagulation Agent Beta-Factor XIIa (M.J. Ramos)
  7. Protein Model Building Using Structural Homology (R.H. Lee)
  8. Protein Motifs and Data-Base Searching (J.M. Thornton)
  9. Rational Reshaping of a Mouse Antibody (A.H. Henry)
  10. "Sequence Analysis Primer" (M. Gribskov)
  11. The De Novo Design of Protein Structures (J.S. Richardson)

Secondary Structure Prediction

  1. Secondary Structure Prediction: Combination of Three Different Methods (V. Biou)

Site-directed mutagenesis

  1. Accurate Prediction of the Stability and Activity Effects of Site-Directed Mutagenesis on a Protein Core (C. Lee)
  2. Evolution of Protein Cores - Constraints in Point Mutations as Observed in Globin Tertiary Structures (D. Bordo)
  3. Suggestions for "Safe" Residue Substitutions in Site-directed Mutagenesis (D. Bordo)

Protein Property Calculations

  1. On the Calculation of pKas in Proteins (A. Yang)

G Protein-Coupled Receptors

  1. A Common Step for Signal Transduction in G Protein-coupled Receptors (L. Oliveira)
  2. A Constitutively Activating Mutation of the Luteinizing Hormone Receptor in Familial Male Precocious Puberty (A. Shenker)
  3. Analysis and Refinement of Criteria for Predicting the Structure and Relative Orientations of Transmembranal Helical Domains (J.A. Ballesteros)
  4. Approaches to Molecular Modeling Studies and Specific Application to Serotonin Ligands and Receptors (R.B. Westkaemper)
  5. Geometry of Proline-Containing Alpha-Helices in Proteins (R. Sankararamakrishnan)
  6. Interactions of Tyr377 in a Ligand-Activation Model of Signal Transmission through Beta 1-Adrenoceptor Alpha-Helices (D. Timms)
  7. Intrahelical Hydrogen Bonding of Serine, Threonine, and Cysteine Residues Within Alpha-Helices and its Relevance to Membrane-bound Proteins (T.M. Gray)
  8. Ligand Selectivity and the Molecular Properties of the 5-HT2 Receptor: Computational Simulations Reveal a Major Role for Transmembrane Helix 7 (D. Zhang)
  9. Model Systems for the Study of Seven-Transmembrane-Segment Receptors (H.G. Dohlman)
  10. Molecular Dynamics of Dopamine at the D2 Receptor (S.G. Dahl)
  11. Molecular Dynamics of Serotonin and Ritanserin Interacting with the 5-HT2 Receptor (O. Edvardsen)
  12. On the Use of the Transmembrane Domain of Bacteriorhodopsin as a Template for Modeling the Three-dimensional Structure of Guanine Nucleotide-Binding Regulatory Protein-Coupled Receptors (L. Pardo)
  13. Projection Structure of Rhodopsin (G.F.X. Schertler)
  14. Proline Kinks in Transmembrane Alpha-Helices (G. von Heijne)
  15. Proline Residues in Transmembrane Helices: Structural or Dynamic Role? (K.A. Williams)
  16. Role of Threonine 342 in Helix 7 of the 5-Hydroxytryptamine Type 1D Receptor in Ligand Binding: An Indirect Mechanism for Receptor Selectivity. (A. Smolyar)
  17. Receptors Coupled to GTP-Binding Proteins, Ligand Binding and G-Protein Activation is a Multistep Dynamic Process (A.D. Strosberg)
  18. Signal Transduction by a 5-HT2 Receptor: A Mechanistic Hypothesis from Molecular Dynamics Simulations of the Three-Dimensional Model of the Receptor Complexed to Ligands (D. Zhang)
  19. Structural and Conformational Features Determining Selective Signal Transduction in the Beta 3-Adrenergic Receptor (N. Blin)
  20. Structure and Function of Receptors Coupled to G Proteins (J.M. Baldwin)
  21. The Evolution and Structure of Aminergic G Protein-coupled Receptors (D. Donnelly)
  22. The Probable Arrangement of the Helices in G Protein-Coupled Receptors (J.M. Baldwin)
  23. Three-Dimensional Modelling of G Protein-Linked Receptors (J. Findlay)

Additional references concerning G-protein coupled receptors can be found in the G Protein-coupled Receptor Database (Harvard Univ.)

Protein Crystallography

  1. "Crystallography Made Crystal Clear" (G. Rhodes)
  2. Human Growth Hormone and Extracellular Domain of its Receptor: Crystal Structure of the Complex (A.M De Vos)
  3. Molecular Architecture and Electrostatic Properties of a Bacterial Porin (M.S. Weiss)
  4. Structural Basis of DNA-Protein Recognition (R.G. Brennan)
  5. X-ray Analyses of Peptide-Inhibitor Complexes Define the Structural Basis of Specificity for Human and Mouse Renins (V. Dhanaraj)

Peptides

  1. Computer Simulations of a Tumor Surface Octapeptide Epitope (R.H. Reid)
  2. Influence of Interatomic Interactions on the Structure and Stability of Polypeptides and Proteins (H. Scheraga)
  3. Prediction of the Native Conformation of a Polypeptide by a Statistical-Mechanical Procedure. I. Backbone Structure of Enkephalin (G.H. Paine)
  4. Use of Buildup and Energy-Minimization Procedures to Compute Low-Energy Structures of the Backbone of Enkephalin (M. Vasquez)

Polysaccharides

  1. Forces in Molecular Recognition: Comparison of Experimental Data and Molecular Mechanics Calculations (J.P. Waltho)
  2. Molecular Dynamics Simulations of Asialoglycoprotein Receptor Ligands (P.V. Balaji)

Nucleic Acids

Software

  1. Computer Graphics Program to Reveal the Dependence of the Gross Three-dimensional Structure of the B-DNA Double Helix on Primary Structure. (C. Tung)
  2. Nucleic Acid Modeling Tool (NAMOT): An Interactive Graphic Tool for Modeling Nucleic Acid Structures (C. Tung)

Structure

  1. Base Sequence, Local Helix Structure, and Macroscopic Curvature of A-DNA and B-DNA (C. Tung)
  2. Computer Graphics and the Generation of DNA Conformations for Intercalation Studies (N.L. Max)
  3. Molecular Mechanical Studies of DNA Flexibility: Coupled Backbone Torsion Angles and Base-Pair Openings (J.W. Keepers)
  4. "Nucleic Acid Geometry and Dynamics" (R.H. Sarma)

Molecular Dynamics of Nucleic Acids

  1. "Nucleic Acid Geometry and Dynamics" (R.H. Sarma)
  2. Toward a Dynamical Structure of DNA: Comparison of Theoretical and Experimental NOE Intensities (J.M. Withka)

Lipids

  1. Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity (R.M Venable)

Docking and Structure-Based Drug Design

Software

  1. GroupBuild: A Fragment-Based Method for De Novo Drug Design (S.H. Rotstein)
  2. Software for Structure-based Drug Design (W.C. Guida)

Methods

  1. A Combinatorial Algorithm for Calculating Ligand Binding (F.S. Kuhl)
  2. A Geometric Approach to Macromolecule-Ligand Interactions (I.D. Kuntz)
  3. A Robust and Efficient Automated Docking Algorithm for Molecular Recognition (N. Kasinos)
  4. Automated DOCKING with Grid-Based Energy Evaluation (E.C. Meng)
  5. Automated Site-Directed Drug Design Using Molecular Lattices (R.A. Lewis)
  6. Functional Group Contributions to Drug-Receptor Interactions (P.R. Andrews)
  7. Molecular Surface Recognition by a Computer Vision-Based Technique (R. Norel)
  8. Molecular Surface Representations by Sparse Critical Points (S.L. Lin)
  9. Structure-Based Molecular Design (I.D. Kuntz)
  10. Structure-Based Strategies for Drug Design and Discovery (I.D. Kuntz)
  11. Surface Motifs by a Computer Vision Technique: Searches, Detection, and Implications for Protein-Ligand Recognition (D. Fischer)

NMR

  1. NMR Studies of Molecular Complexes as a Tool in Drug Design (S.W. Fesik)

Nucleic Acid Ligands

  1. Computer Graphics and the Generation of DNA Conformations for Intercalation Studies (N.L. Max)
  2. Interactions of Molecules with Nucleic Acids. VII. Evaluation and Presentation of Steric Contours and Molecules in Bonding Sites (K.J. Miller)
  3. Predicted Mode of Intercalation of Doxorubicin with Dinucleotide Dimers (Y. Nakata)

Protein Ligands

  1. Structure-Based Discovery of Inhibitors of Thymidylate Synthase (B.K. Shoichet)
  2. Structure-Based Inhibitor Design by Using Protein Models for the Development of Antiparasitic Agents (C.S. Ring)