the goodman group
university of cambridge  


   references & suggested reading

Tinker


15. References & Suggested Reading

This section contains a list of the references to general theory, algorithms and implementation details which have been of use during the development of the TINKER package. Methods described in some of the references have been implemented in detail within the TINKER source code. Other references contain useful background information although the algorithms themselves are now obsolete. Still other papers contain ideas or extensions planned for future inclusion in TINKER. References for specific force field parameter sets are provided in an earlier section of this User's Guide. This list is heavily skewed toward biomolecules in general and proteins in particular. This bias reflects our group's major interests; however an attempt has been made to include methods which should be generally applicable.

PARTIAL LIST OF MOLECULAR MECHANICS SOFTWARE PACKAGES

AMBER
Peter Kollman, University of California, San Francisco

AMMP
Rob Harrison, Thomas Jefferson University, Philadelphia

ARGOS
Andy McCammon, University of California, San Diego

BOSS
William Jorgensen, Yale University

BRUGEL
Shoshona Wodak, Free University of Brussels

CFF
Shneior Lifson, Weizmann Institute

CHARMM
Martin Karplus, Harvard University

CHARMM/GEMM
Bernard Brooks, National Institutes of Health, Bethesda

DELPHI
Bastian van de Graaf, Delft University of Technology

DISCOVER
Molecular Simulations Inc., San Diego

DL_POLY
W. Smith & T. Forester, CCP5, Daresbury Laboratory

ECEPP
Harold Scheraga, Cornell University

ENCAD
Michael Levitt, Stanford University

FANTOM
Werner Braun, University of Texas, Galveston

FEDER/2
Nobuhiro Go, Kyoto University

GROMACS
Herman Berendsen, University of Groningen

GROMOS
Wilfred van Gunsteren, BIOMOS and ETH, Zurich

IMPACT
Ronald Levy, Rutgers University

MACROMODEL
Schodinger, Inc., Jersey City, New Jersey

MM2/MM3/MM4
N. Lou Allinger, University of Georgia

MMC
Cliff Dykstra, Indiana Univ.-Purdue Univ. at Indianapolis

MMFF
Tom Halgren, Merck Research Laboratories, Rahway

MMTK
Konrad Hinsen, Inst. of Structural Biology, Grenoble

MOIL
Ron Elber, Cornell University

MOLARIS
Arieh Warshal, University of Southern California

MOLDY
Keith Refson, Oxford University

MOSCITO
Dietmar Paschek & Alfons Geiger, Universität Dortmund

NAMD
Klaus Schulten, University of Illinois, Urbana

OOMPAA
Andy McCammon, University of California, San Diego

ORAL
Karel Zimmerman, INRA, Jouy-en-Josas, France

ORIENT
Anthony Stone, Cambridge University

PCMODEL
Kevin Gilbert, Serena Software, Bloomington, Indiana

PEFF
Jan Dillen, University of Pretoria, South Africa

Q
Johan Åqvist, Uppsala University

SIBFA
Nohad Gresh, INSERM, CNRS, Paris

SIGMA
Jan Hermans, University of North Carolina

SPASIBA
Gerard Vergoten, Université de Lille

SPASMS
David Spellmeyer and the Kollman Group, UCSF

TINKER
Jay Ponder, Washington University, St. Louis

XPLOR/CNS
Axel Brünger, Stanford University

YAMMP
Stephen Harvey, University of Alabama, Birmingham

YASP
Florian Mueller-Plathe, ETH Zentrum, Zurich

YETI
Angelo Vedani, Biografik-Labor 3R, Basel

AMBER
D. A Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman, AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules, Comp. Phys. Commun. , 91, 1-41 (1995)

ARGOS
T. P. Straatsma and J. A. McCammon, ARGOS, a Vectorized General Molecular Dynamics Program, J. Comput. Chem. , 11, 943-951 (1990)

CHARMM
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comput. Chem. , 4, 187-217 (1983)

ENCAD
M. Levitt, M. Hirshberg, R. Sharon and V. Daggett, Potential Energy Function and Parameters for Simulations for the Molecular Dynamics of Proteins and Nucleic Acids in Solution, Comp. Phys. Commun. , 91, 215-231 (1995)

FANTOM
T. Schaumann, W. Braun and K. Wurtrich, The Program FANTOM for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in Torsion Angle Space, Biopolymers, 29, 679-694 (1990)

FEDER/2
H. Wako, S. Endo, K. Nagayama and N. Go, FEDER/2: Program for Static and Dynamic Conformational Energy Analysis of Macro-molecules in Dihedral Angle Space, Comp. Phys. Commun. , 91, 233-251 (1995)

GROMACS
H. J. C. Berendsen, D. van der Spoel and R. van Drunen, GROMACS: A Message-passing Parallel Molecular Dynamics Implementation, Comp. Phys. Commun. , 91, 43-56 (1995)

GROMOS W. R. P. Scott, P. H. Hunenberger , I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Kruger, W. F. van Gunsteren, The GROMOS Biomolecular Simulation Program Package, J. Phys. Chem. A, 103, 3596-3607 (1999)

IMPACT
D. B. Kitchen, F. Hirata, J. D. Westbrook, R. Levy, D. Kofke and M. Yarmush, Conserving Energy during Molecular Dynamics Simulations of Water, Proteins, and Proteins in Water, J. Comput. Chem. , 10, 1169-1180 (1990)

MACROMODEL
F. Mahamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson and W. C. Still, MacroModel-An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics, J. Comput. Chem. , 11, 440-467 (1990)

MM2
N. L. Allinger, Conformational Analysis. 130. MM2. A Hydrocarbon Force Field Utilizing V1 and V2 Torsional Terms, J. Am. Chem. Soc. , 99, 8127-8134 (1977)

MM3
N. L. Allinger, Y. H. Yuh and J.-H. Lii, Molecular Mechanics. The MM3 Force Field for Hydrocarbons, J. Am. Chem. Soc. , 111, 8551-8566 (1989)

MM4
N. L. Allinger, K. Chen and J.-H. Lii, An Improved Force Field (MM4)

for Saturated Hydrocarbons, J. Comput. Chem. , 17, 642-668 (1996)

MMC
C. E. Dykstra, Molecular Mechanics for Weakly Interacting Assemblies of Rare Gas Atoms and Small Molecules, J. Am. Chem. Soc. , 111, 6168-6174 (1989)

MMFF
T. A. Halgren, Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94, J. Comput. Chem. , 17, 490-516 (1996)

MOIL
R. Elber, A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhiver, C. Keasar, J. Zhang and A. Ulitsky, MOIL: A Program for Simulations of Macromolecules, Comp. Phys. Commun., 91, 159-189 (1995)

MOSCITO
See the web site at http:/ganter.chemie.uni-dortmund.de/~pas/moscito.html

NAMD
L. Kalé, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan and K. Schulten, NAMD2: Greater Scalability for Parallel Molecular Dynamics, J. Comput. Phys. , 151, 283-312 (1999)

OOMPAA
G. A. Huber and J. A. McCammon, OOMPAA-Object-oriented Model for Probing Assemblages of Atoms, J. Comput. Phys. , 151, 264-282 (1999)

ORAL
K. Zimmermann, ORAL: All Purpose Molecular Mechanics Simulator and Energy Minimizer, J. Comput. Chem. , 12, 310-319 (1991)

PCMODEL
See the web site at http:/www.serenasoft.com

PEFF
J. L. M. Dillen, PEFF: A Program for the Development of Empirical Force Fields, J. Comput. Chem. , 13, 257-267 (1992)

Q
See the web site at http://aqvist.bmc.uu.se/Q

SIBFA
N. Gresh, Inter- and Intramolecular Interactions. Inception and Refinements of the SIBFA, Molecular Mechanics (SMM)

Procedure, a Separable, Polarizable Methodology Grounded on ab Initio SCF/MP2 Computations. Examples of Applications to Molecular Recognition Problems, J. Chim. Phys. PCB , 94, 1365-1416 (1997)

SIGMA
See the web site at http://femto.med.unc.edu/SIGMA

SPASIBA
P. Derreumaux and G. Vergoten, A New Spectroscopic Molecular Mechanics Force-Field - Parameters For Proteins, J. Chem. Phys. , 102, 8586-8605 (1995)

TINKER
See the web site at http://dasher.wustl.edu/tinker

YAMMP
R. K.-Z. Tan and S. C. Harvey, Yammp: Development of a Molecular Mechanics Program Using the Modular Programming Method, J. Comput. Chem. , 14, 455-470 (1993)

YETI
A. Vedani, YETI: An Interactive Molecular Mechanics Program for Small-Molecule Protein Complexes, J. Comput. Chem. , 9, 269-280 (1988)


MOLECULAR MECHANICS

U. Burkert and N. L. Allinger, Molecular Mechanics , American Chemical Society, Washington, D.C., 1982

K. Rasmussen, Potential Energy Functions in Conformational Analysis (Lecture Notes in Chemistry, Vol. 27)

, Springer-Verlag, Berlin, 1985

A. K. Rappé and C. J. Casewit, Molecular Mechanics across Chemistry , University Science Books, Sausalito, CA, 1997

K. Machida, Principles of Molecular Mechanics , Kodansha/John Wiley & Sons, Tokyo/New York, 1999

P. Comba and T. W. Hambley, Molecular Modeling of Inorganic Compounds , VCH, New York, 1995

COMPUTER SIMULATION METHODS

M. J. Field, A Practical Introduction to the Simulation of Molecular Systems, Cambridge Univ. Press, Cambridge, 1999

A. R. Leach, Molecular Modelling: Principles and Applications , Addison Wesley Longman, Essex, England, 1996

D. Frankel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, Academic Press, San Diego, CA, 1996

D. C. Rapaport, The Art of Molecular Dynamics Simulation , Cambridge University Press, Cambridge, 1995

J. M. Haile, Molecular Dynamics Simulation , John Wiley and Sons, New York, 1992

M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids , Oxford University Press, Oxford, 1987

T. Schlick, R. D. Skeel, A. T. Brünger, L. V. Kale, J. A. Board, J. Hermans and K. Schulten, Algorithmic Challenges in Computational Molecular Biophysics, J. Comput. Phys. , 151, 9- 48 (1999)

MODELING OF BIOLOGICAL MACROMOLECULES

J. A. McCammon and S. Harvey, Dynamics of Proteins and Nucleic Acids , Cambridge University Press, Cambridge, 1987

C. L. Brooks III, M. Karplus and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics , John Wiley and Sons, New York, 1988

W. F. van Gunsteren, P. K. Weiner and A. J. Wilkinson, Computer Simulation of Biomolecular Systems, Vol. 1-3 , Kluwer Academic Publishers, Dordrecht, 1989-1997

T. E. Cheatham and B. R. Brooks, Recent Advances in Molecular Dynamics Simulation towards the Realistic Representation of Biomolecules in Solution, Theor. Chem. Acc. , 99, 279-288 (1998)

CONJUGATE GRADIENT AND QUASI-NEWTON OPTIMIZATION

J. Nocedal and S. J. Wright, Numerical Optimization , Springer-Verlag, New York, 1999

S. G. Nash and A. Sofer, Linear and Nonlinear Programming , McGraw-Hill, New York, 1996

R. Fletcher, Practical Methods of Optimization , John Wiley & Sons Ltd., Chichester, 1987

D. G. Luenberger, Linear and Nonlinear Programming , 2nd Ed., Addison-Wesley, Reading, MA, 1984

P. E. Gill, W. Murray and M. H. Wright, Practical Optimization , Academic Press, New York, 1981

J. Nocedal, Updating Quasi-Newton Matrices with Limited Storage, Math. Comp. , 773-782 (1980)

S. J. Watowich, E. S. Meyer, R. Hagstrom and R. Josephs, A Stable, Rapidly Converging Conjugate Gradient Method for Energy Minimization, J. Comput. Chem. , 9, 650-661 (1988)

W. C. Davidon, Optimally Conditioned Optimization Algorithms without Line Searches, Math. Prog. , 9, 1-30 (1975)

TRUNCATED NEWTON OPTIMIZATION

J. W. Ponder and F. M. Richards, An Efficient Newton-like Method for Molecular Mechanics Energy Minimization of Large Molecules, J. Comput. Chem. , 8, 1016-1024 (1987)

R. S. Dembo and T. Steihaug, Truncated-Newton Algorithms for Large-Scale Unconstrained Optimization, Math. Prog. , 26, 190-212 (1983)

S. C. Eisenstat and H. F. Walker, Choosing the Forcing Terms in an Inexact Newton Method, SIAM J. Sci. Comput. , 17, 16-32 (1996)

T. Schlick and M. Overton, A Powerful Truncated Newton Method for Potential Energy Minimization, J. Comput. Chem. , 8, 1025-1039 (1987)

D. S. Kershaw, The Incomplete Cholesky-Conjugate Gradient Method for the Iterative Solution of Systems of Linear Equations, J. Comput. Phys. , 26, 43-65 (1978)

T. A. Manteuffel, An Incomplete Factorization Technique for Positive Definite Linear Systems, Math. Comp. , 34, 473-497 (1980)

P. Derreumaux, G. Zhang and T. Schlick and B. R. Brooks, A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications, J. Comput. Chem. , 15, 532-552 (1994)

I. S. Duff, A. M. Erisman and J. K. Reid, Direct Methods for Sparse Matrices , Oxford University Press, Oxford, 1986

POTENTIAL ENERGY SMOOTHING

R. V. Pappu, R. K. Hart and J. W. Ponder, Analysis and Application of Potential Energy Smoothing Methods for Global Optimization, J. Phys. Chem. B , 102, 9725-9742 (1998)

L. Piela, J. Kostrowicki and H. A. Scheraga, The Multiple-Minima Problem in the Conformational Analysis of Molecules. Deformation of the Potential Energy Hypersurface by the Diffusion Equation Method, J. Phys. Chem. , 93, 3339-3346 (1989)

J. Ma and J. E. Straub, Simulated Annealing Using the Classical Density Distribution, J. Chem. Phys. , 101, 533-541 (1994)

C. Tsoo and C. L. Brooks, Cluster Structure Determination Using Gaussian Density Distribution Global Minimization Methods, J. Chem. Phys. , 101, 6405-6411 (1994)

S. Nakamura, H. Hirose, M. Ikeguchi and J. Doi, Conformational Energy Minimization Using a Two-Stage Method, J. Phys. Chem. , 99, 8374-8378 (1995)

T. Huber, A. E. Torda and W. F. van Gunsteren, Structure Optimization Combining Soft- Core Interaction Functions, the Diffusion Equation Method, and Molecular Dynamics, J. Phys. Chem. A , 101, 5926-5930 (1997)

S. Schelstraete and H. Verschelde, Finding Minimum-Energy Configurations of Lennard- Jones Clusters Using an Effective Potential, J. Phys. Chem. A , 101, 310-315 (1998)

I. Andricioaei and J. E. Straub, Global Optimization Using Bad Derivatives: Derivative-Free Method for Molecular Energy Minimization, J. Comput. Chem. , 19, 1445-1455 (1998)

L. Piela, Search for the Most Stable Structures on Potential Energy Surfaces, Coll. Czech. Chem. Commun. , 63, 1368-1380 (1998)

"SNIFFER" GLOBAL OPTIMIZATION

A. O. Griewank, Generalized Descent for Global Optimization, J. Opt. Theor. Appl. , 34, 11- 39 (1981)

R. A. R. Butler and E. E. Slaminka, An Evaluation of the Sniffer Global Optimization Algorithm Using Standard Test Functions, J. Comput. Phys. , 99, 28-32 (1993)

J. W. Rogers and R. A. Donnelly, Potential Transformation Methods for Large-Scale Global Optimization, SIAM J. Optim. , 5, 871-891 (1995)

INTEGRATION METHODS FOR MOLECULAR DYNAMICS

D. Beeman, Some Multistep Methods for Use in Molecular Dynamics Calculations, J. Comput. Phys. , 20, 130-139 (1976)

M. Levitt and H. Meirovitch, Integrating the Equations of Motion, J. Mol. Biol. , 168, 617- 620 (1983)

J. Aqvist, W. F. van Gunsteren, M. Leijonmarck and O. Tapia, A Molecular Dynamics Study of the C-Terminal Fragment of the L7/L12 Ribosomal Protein, J. Mol. Biol. , 183, 461-477 (1985)

W. C. Swope, H. C. Andersen, P. H. Berens and K. R. Wilson, A Computer Simulation Method for the Calculation of Equilibrium Constants for the Formation of Physical Clusters of Molecules: Application to Small Water Clusters, J. Chem. Phys. , 76, 637-649 (1982)

CONSTRAINT DYNAMICS

W. F. van Gunsteren and H. J. C. Berendsen, Algorithms for Macromolecular Dynamics and Constraint Dynamics, Mol. Phys. , 34, 1311-1327 (1977)

G. Ciccotti, M. Ferrario and J.-P. Ryckaert, Molecular Dynamics of Rigid Systems in Cartesian Coordinates: A General Formulation, Mol. Phys. , 47, 1253-1264 (1982)

H. C. Andersen, Rattle: A "Velocity" Version of the Shake Algorithm for Molecular Dynamics Calculations, J. Comput. Phys. , 52, 24-34 (1983)

R. Kutteh, RATTLE Recipe for General Holonomic Constraints: Angle and Torsion Constraints, CCP5 Newsletter , 46, 9-17 (1998)

[available from the web site at http://www.dl.ac.uk/CCP/CCP5/newsletter_index.html] B. J. Palmer, Direct Application of SHAKE to the Velocity Verlet Algorithm, J. Comput. Phys., 104, 470-472 (1993)

S. Miyamoto and P. A. Kollman, SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models, J. Comput. Chem. , 13, 952-962 (1992)

B. Hess, H. Bekker, H. J. C. Berendsen and J. G. E. M. Fraaije, LINCS: A Linear Constraint Solver for Molecular Simulations, J. Comput. Chem. , 18, 1463-1472 (1997)

J. T. Slusher and P. T. Cummings, Non-Iterative Constraint Dynamics using Velocity- Explicit Verlet Methods, Mol. Simul. , 18, 213-224 (1996)

LANGEVIN, BROWNIAN AND STOCHASTIC DYNAMICS

M. P. Allen, Brownian Dynamics Simulation of a Chemical Reaction in Solution, Mol. Phys. , 40, 1073-1087 (1980)

W. F. van Gunsteren and H. J. C. Berendsen, Algorithms for Brownian Dynamics, Mol. Phys., 45, 637-647 (1982)

F. Guarnieri and W. C. Still, A Rapidly Convergent Simulation Method: Mixed Monte Carlo/Stochastic Dynamics, J. Comput. Chem. , 15, 1302-1310 (1994)

M. G. Paterlini and D. M. Ferguson, Constant Temperature Simulations using the Langevin Equation with Velocity Verlet Integration, Chem. Phys. , 236, 243-252 (1998)

CONSTANT TEMPERATURE AND PRESSURE DYNAMICS

H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola and J. R. Haak, Molecular Dynamics with Coupling to an External Bath, J. Chem. Phys. , 81, 3684-3690 (1984)

W. G. Hoover, Canonical Dynamics: Equilibrium Phase-space Distributions, Phys. Rev. A , 31, 1695-1697 (1985)

J. J. Morales, S. Toxvaerd and L. F. Rull, Computer Simulation of a Phase Transition at Constant Temperature and Pressure, Phys. Rev. A , 34, 1495-1498 (1986)

B. R. Brooks, Algorithms for Molecular Dynamics at Constant Temperature and Pressure, Internal Report of Division of Computer Research and Technology, National Institutes of Health, 1988. M. Levitt, Molecular Dynamics of Native Protein: Computer Simulation of Trajectories, J. Mol. Biol. , 168, 595-620 (1983)

OUT-OF-PLANE DEFORMATION TERMS

J. R. Maple, U. Dinar and A. T. Hagler, Derivation of Force Fields for Molecular Mechanics and Dynamics from ab initio Energy Surfaces, Proc. Natl. Acad. Sci. USA , 85, 5350-5354 (1988)

S.-H. Lee, K. Palmo and S. Krimm, New Out-of-Plane Angle and Bond Angle Internal Coordinates and Related Potential Energy Functions for Molecular Mechanics and Dynamics Simulations, J. Comput. Chem. , 20, 1067-1084 (1999)

ANALYTICAL DERIVATIVES OF POTENTIAL FUNCTIONS

K. J. Miller, R. J. Hinde and J. Anderson, First and Second Derivative Matrix Elements for the Stretching, Bending, and Torsional Energy, J. Comput. Chem. , 10, 63-76 (1989)

D. H. Faber and C. Altona, UTAH5: A Versatile Programme Package for the Calculation of Molecular Properties by Force Field Methods, Computers & Chemistry , 1, 203-213 (1977)

W. C. Swope and D. M. Ferguson, Alternative Expressions for Energies and Forces Due to Angle Bending and Torsional Energy, Report G320-3561, J. Comput. Chem. , 13, 585-594 (1992)

A. Blondel and M. Karplus, New Formulation for Derivatives of Torsion Angles and Improper Torsion Angles in Molecular Mechanics: Elimination of Singularities, J. Comput. Chem., 17, 1132-1141 (1996)

R. E. Tuzun, D. W. Noid and B. G. Sumpter, Efficient Treatment of Out-of-Plane Bend and Improper Torsion Interactions in MM2, MM3, and MM4 Molecular Mechanics Calculations, J. Comput. Chem. , 18, 1804-1811 (1997)

TORSIONAL SPACE DERIVATIVES AND NORMAL MODES

M. Levitt, C. Sander and P. S. Stern, Protein Normal-mode Dynamics: Trypsin Inhibitor, Crambin, Ribonuclease and Lysozyme, J. Mol. Biol. , 181, 423-447 (1985)

M. Levitt, Protein Folding by Restrained Energy Minimization and Molecular Dynamics, J. Mol. Biol. , 170, 723-764 (1983)

H. Wako and N. Go, Algorithm for Rapid Calculation of Hessian of Conformational Energy Function of Proteins by Supercomputer, J. Comput. Chem. , 8, 625-635 (1987)

H. Abe, W. Braun, T. Noguti and N. Go, Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins: General Recurrent Equations, Computers & Chemistry , 8, 239-247 (1984)

T. Noguti and N. Go, A Method of Rapid Calculation of a Second Derivative Matrix of Conformational Energy for Large Molecules, J. Phys. Soc. Japan , 52, 3685-3690 (1983)

ANALYTICAL SURFACE AREA AND VOLUME

M. L. Connolly, Analytical Molecular Surface Calculation, J. Appl. Cryst. , 16, 548-558 (1983)

M. L. Connolly, Computation of Molecular Volume, J. Am. Chem. Soc. , 107, 1118-1124 (1985)

M. L. Connolly, Molecular Surfaces: A Review, available from the web site at http://www.netsci.org/Science/Compchem/feature14.html C. E. Kundrot, J. W. Ponder and F. M. Richards, Algorithms for Calculating Excluded Volume and Its Derivatives as a Function of Molecular Conformation and Their Use in Energy Minimization, J. Comput. Chem. , 12, 402-409 (1991)

T. J. Richmond, Solvent Accessible Surface Area and Excluded Volume in Proteins, J. Mol. Biol., 178, 63-89 (1984)

L. Wesson and D. Eisenberg, Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution, Protein Science , 1, 227-235 (1992)

V. Gononea and E. Osawa, Implementation of Solvent Effect in Molecular Mechanics, Part 3. The First- and Second-order Analytical Derivatives of Excluded Volume, J. Mol. Struct. (Theochem)

, 311 305-324 (1994)

K. D. Gibson and H. A. Scheraga, Exact Calculation of the Volume and Surface Area of Fused Hard-sphere Molecules with Unequal Atomic Radii, Mol. Phys. , 62, 1247-1265 (1987)

K. D. Gibson and H. A. Scheraga, Surface Area of the Intersection of Three Spheres with Unequal Radii: A Simplified Analytical Formula, Mol. Phys. , 64, 641-644 (1988)

S. Sridharan, A. Nichols and K. A. Sharp, A Rapid Method for Calculating Derivatives of Solvent Accessible Surface Areas of Molecules, J. Comput, Chem. , 16, 1038-1044 (1995)

APPROXIMATE SURFACE AREA AND VOLUME

S. J. Wodak and J. Janin, Analytical Approximation to the Accessible Surface Area of Proteins, Proc. Natl. Acad. Sci. USA , 77, 1736-1740 (1980)

W. Hasel, T. F. Hendrickson and W. C. Still, A Rapid Approximation to the Solvent Accessible Surface Areas of Atoms, Tetrahedron Comput. Method. , 1, 103-116 (1988)

J. Weiser, P. S. Shenkin and W. C. Still, Approximate Solvent-Accessible Surface Areas from Tetrahedrally Directed Neighber Densities, Biopolymers, 50, 373-380 (1999)

BOUNDARY CONDITIONS AND NEIGHBOR METHODS

W. F. van Gunsteren, H. J. C. Berendsen, F. Colonna, D. Perahia, J. P. Hollenberg and D. Lellouch, On Searching Neighbors in Computer Simulations of Macromolecular Systems, J. Comput. Chem. , 5, 272-279 (1984)

F. Sullivan, R. D. Mountain and J. O'Connell, Molecular Dynamics on Vector Computers, J. Comput. Phys. , 61, 138-153 (1985)

J. Boris, A Vectorized "Near Neighbors" Algorithm of Order N Using a Monotonic Logical Grid, J. Comput. Phys. , 66, 1-20 (1986)

S. G. Lambrakos and J. P. Boris, Geometric Properties of the Monotonic Lagrangian Grid Algorithm for Near Neighbors Calculations, J. Comput. Phys. , 73, 183-202 (1987)

T. A. Andrea, W. C. Swope and H. C. Andersen, The Role of Long Ranged Forces in Determining the Structure and Properties of Liquid Water, J. Chem. Phys. , 79, 4576-4584 (1983)

D. N. Theodorou and U. W. Suter, Geometrical Considerations in Model Systems with Periodic Boundary Conditions, J. Chem. Phys. , 82, 955-966 (1985)

J. Barnes and P. Hut, A Hierarchical O(NlogN)

Force-calculation Algorithm, Nature, 234, 446-449 (1986)

CUTOFF AND TRUNCATION METHODS

P. J. Steinbach and B. R. Brooks, New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation, J. Comput. Chem. , 15, 667-683 (1993)

R. J. Loncharich and B. R. Brooks, The Effects of Truncating Long-Range Forces on Protein Dynamics, Proteins, 6, 32-45 (1989)

C. L. Brooks III, B. M. Pettitt and M. Karplus, Structural and Energetic Effects of Truncating Long Ranged Interactions in Ionic and Polar Fluids, J. Chem. Phys. , 83, 5897- 5908 (1985)

EWALD SUMMATION TECHNIQUES

A. Y. Toukmaji and J. A. Board, Jr., Ewald Summation Techniques in Perspective: A Survey, Comp. Phys. Commun. , 95, 73-92 (1996)

T. Darden, L. Perera, L. Li and L. Pedersen, New Tricks for Modelers from the Crystallography Toolkit: The Particle Mesh Ewald Algorithm and its Use in Nucleic Acid Simulations, Structure, 7, R550-R60 (1999)

T. Darden, D. York and L. G. Pedersen, Particle Mesh Ewald: An N·log( N)

Method for Ewald Sums in Large Systems, J. Chem. Phys. , 98, 10089-10092 (1993)

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen, A Smooth Particle Mesh Ewald Method, J. Chem. Phys. , 103, 8577-8593 (1995)

W. Smith, Point Multipoles in the Ewald Summation (Revisited), CCP5 Newsletter , 46, 18- 30 (1998)

[available from http://www.dl.ac.uk/CCP/CCP5/newsletter_index.html] S. E. Feller, R. W. Pastor, A. Rojnuckarin, S. Bogusz and B. R. Brooks, Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water, J. Phys. Chem. , 100, 17011-17020 (1996)

W. Weber, P. H. Hünenberger and J. A. McCammon, Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation, J. Phys. Chem. B , 104, 3668-3675 (2000)

CONJUGATED AND AROMATIC SYSTEMS

N. L. Allinger, F. Li, L. Yan and J. C. Tai, Molecular Mechanics (MM3)

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J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, The MMP2 Calculational Method, J. Comput. Chem. , 8, 581-603 (1987)

J. Kao, A Molecular Orbital Based Molecular Mechanics Approach to Study Conjugated Hydrocarbons, J. Am. Chem. Soc. , 109, 3818-3829 (1987)

J. Kao and N. L. Allinger, Conformational Analysis: Heats of Formation of Conjugated Hydrocarbons by the Force Field Method, J. Am. Chem. Soc. , 99, 975-986 (1977)

D. H. Lo and M. A. Whitehead, Accurate Heats of Atomization and Accurate Bond Lengths: Benzenoid Hydrocarbons, Can. J. Chem. , 46, 2027-2040 (1968)

G. D. Zeiss and M. A. Whitehead, Hetero-atomic Molecules: Semi-empirical Molecular Orbital Calculations and Prediction of Physical Properties, J. Chem. Soc. A , 1727-1738 (1971)

FREE ENERGY SIMULATION METHODS

P. Kollman, Free Energy Calculations: Applications to Chemical and Biochemical Phenomena, Chem. Rev. , 93, 2395-2417 (1993)

B. L. Tembe and J. A. McCammon, Ligand-Receptor Interactions, Computers & Chemistry , 8, 281-283 (1984)

W. L. Jorgensen and C. Ravimohan, Monte Carlo Simulation of Differences in Free Energy of Hydration, J. Chem. Phys. , 83, 3050-3054 (1985)

W. L. Jorgensen, J. K. Buckner, S. Boudon and J. Tirado-Rives, Efficient Computation of Absolute Free Energies of Binding by Computer Simulations: Application to the Methane Dimer in Water, J. Chem. Phys. , 89, 3742-3746 (1988)

S. H. Fleischman and C. L. Brooks III, Thermodynamics of Aqueous Solvation: Solution Properties of Alcohols and Alkanes, J. Chem. Phys. , 87, 3029-3037 (1987)

U. C. Singh, F. K. Brown, P. A. Bash and P. A. Kollman, An Approach to the Application of Free Energy Perturbation Methods Using Molecular Dynamics, J. Am. Chem. Soc. , 109, 1607-1614 (1987)

D. A. Pearlman and P. A. Kollman, A New Method for Carrying out Free Energy Perturbation Calculations: Dynamically Modified Windows, J. Chem. Phys. , 90, 2460-2470 (1989)

T. P. Straatsma, H. J. C. Berendsen and J. P. M. Postma, Free Energy of Hydrophobic Hydration: A Molecular Dynamics Study of Noble Gases in Water, J. Chem. Phys. , 85, 6720-6727 (1986)

T. P. Straatsma and H. J. C. Berendsen, Free Energy of Ionic Hydration: Analysis of a Thermodynamic Integration Technique to Evaluate Free Energy Differences by Molecular Dynamics Simulations, J. Chem. Phys. , 89, 5876-5886 (1988)

M. Mezei, The Finite Difference Thermodynamic Integration, Tested on Calculating the Hydration Free Energy Difference between Acetone and Dimethylamine in Water, J. Chem. Phys., 86, 7084-7088 (1987)

A. E. Mark and W. F. van Gunsteren, Decomposition of the Free Energy of a System in Terms of Specific Interactions, J. Mol. Biol. , 240, 167-176 (1994)

S. Boresch and M. Karplus, The Meaning of Copmponent Analysis: Decomposition of the Free Energy in Terms of Specific Interactions, J. Mol. Biol. , 254, 801-807 (1995)

METHODS FOR PARAMETER DETERMINATION

N. L. Allinger, X. Zhou and J. Bergsma, Molecular Mechanics Parameters, J. Mol. Struct. (THEOCHEM), 312, 69-83 (1994)

A. J. Pertsin and A. I. Kitaigorodsky, The Atom-Atom Potential Method: Application to Organic Molecular Solids , Springer-Verlag, Berlin, 1987

D. E. Williams, Transferable Empirical Nonbonded Potential Functions, in Crystal Cohesion and Conformational Energies , Ed. by R. M. Metzger, Springer-Verlag, Berlin, 1981

A. T. Hagler and S. Lifson, A Procedure for Obtaining Energy Parameters from Crystal Packing, Acta Cryst. , B30, 1336-1341 (1974)

A. T. Hagler, S. Lifson and P. Dauber, Consistent Force Field Studies of Intermolecular Forces in Hydrogen-Bonded Crystals: A Benchmark for the Objective Comparison of Alternative Force Fields, J. Am. Chem. Soc. , 101, 5122-5130 (1979)

W. L. Jorgensen, J. D. Madura and C. J. Swenson, Optimized Intermolecular Potential Functions for Liquid Hydrocarbons, J. Am. Chem. Soc. , 106, 6638-6646 (1984)

W. L. Jorgensen and C. J. Swenson, Optimized Intermolecular Potential Functions for Amides and Peptides: Structure and Properties of Liquid Amides, J. Am. Chem. Soc. , 107, 569-578 (1985)

J. R. Maple, U. Dinur and A. T. Hagler, Derivation of Force Fields for Molecular Mechanics and Dynamics from ab Initio Surfaces, Proc. Nat. Acad. Sci. USA , 85, 5350-5354 (1988)

U. Dinur and A. T. Hagler, Direct Evaluation of Nonbonding Interactions from ab Initio Calculations, J. Am. Chem. Soc. , 111, 5149-5151 (1989)

ELECTROSTATIC INTERACTIONS

S. L. Price, Towards More Accurate Model Intermolecular Potentials for Organic Molecules, Rev. Comput. Chem. , 14, 225-289 (2000)

C. H. Faerman and S. L. Price, A Transferable Distributed Multipole Model for the Electrostatic Interactions of Peptides and Amides, J. Am. Chem. Soc. , 112, 4915-4926 (1990)

C. E. Dykstra, Electrostatic Interaction Potentials in Molecular Force Fields, Chem. Rev. , 93, 2339-2353 (1993)

M. J. Dudek and J. W. Ponder, Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins, J. Comput. Chem. , 16, 791-816 (1995)

U. Koch and E. Egert, An Improved Description of the Molecular Charge Density in Force Fields with Atomic Multipole Moments, J. Comput. Chem. , 16, 937-944 (1995)

D. E. Williams, Representation of the Molecular Electrostatic Potential by Atomic Multipole and Bond Dipole Models, J. Comput. Chem. , 9, 745-763 (1988)

F. Colonna, E. Evleth and J. G. Angyan, Critical Analysis of Electric Field Modeling: Formamide, J. Comput. Chem. , 13, 1234-1245 (1992)

POLARIZATION EFFECTS

S. Kuwajima and A. Warshel, Incorporating Electric Polarizabilities in Water-Water Interaction Potentials, J. Phys. Chem. , 94, 460-466 (1990)

J. W. Caldwell and P. A. Kollman, Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide, J. Phys. Chem., 99, 6208-6219 (1995)

D. N. Bernardo, Y. Ding, K. Kroegh-Jespersen and R. M. Levy, An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields, J. Phys. Chem. , 98, 4180-4187 (1994)

P. T. van Duijnen and M. Swart, Molecular and Atomic Polarizabilities: Thole's Model Revisited, J. Phys. Chem. A , 102, 2399-2407 (1998)

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J. Applequist, Atom Charge Transfer in Molecular Polarizabilities. Application of the Olson- Sundberg Model to Aliphatic and Aromatic Hydrocarbons, J. Phys. Chem. , 97, 6016-6023 (1993)

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J. M. Stout and C. E. Dykstra, A Distributed Model of the Electrical Response of Organic Molecules, J. Phys. Chem. A , 102, 1576-1582 (1998)

MACROSCOPIC TREATMENT OF SOLVENT

C. J. Cramer and D. G. Truhlar, Continuum Solvation Models: Classical and Quantum Mechanical Implementations, Rev. Comput. Chem. , 6, 1-72 (1995)

B.Roux and T. Simonson, Implicit Solvation Models, Biophys. Chem. , 78, 1-20 (1999)

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SURFACE AREA-BASED SOLVATION MODELS

D. Eisenberg and A. D. McLachlan, Solvation Energy in Protein Folding and Binding, Nature, 319, 199-203 (1986)

L. Wesson and D. Eisenberg, Atomic Solvation Parameters Applied to Molecular Dynamics of Proteins in Solution, Prot. Sci. , 1, 227-235 (1992)

T. Ooi, M. Oobatake, G. Nemethy and H. A. Scheraga, Accessible Surface Areas as a Measure of the Thermodynamic Parameters of Hydration of Peptides, Proc. Natl. Acad. Sci. USA , 84, 3086-3090 (1987)

J. D. Augspurger and H. A. Scheraga, An Efficient, Differentiable Hydration Potential for Peptides and Proteins, J. Comput. Chem. , 17, 1549-1558 (1996)

GENERALIZED BORN SOLVATION MODELS

W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson, A Semiempirical Treatment of Solvation for Molecular Mechanics and Dynamics, J. Am. Chem. Soc. , 112, 6127-6129 (1990)

D. Qiu, P. S. Shenkin, F. P. Hollinger and W. C. Still, The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii, J. Phys. Chem. A , 101, 3005-3014 (1997)

G. D. Hawkins, C. J. Cramer and D. G. Truhlar, Pairwise Solute Descreening of Solute Charges from a Dielectric Medium, Chem. Phys. Lett. , 246, 122-129 (1995)

G. D. Hawkins, C. J. Cramer and D. G. Truhlar, Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium, J. Phys. Chem. , 100, 19824-19839 (1996)

A. Onufriev, D. Bashford and D. A. Case, Modification of the Generalized Born Model Suitable for Macromolecules, J. Phys. Chem. B , 104, 3712-3720 (2000)

M. Schaefer and M. Karplus, A Comprehensive Analytical Treatment of Continuum Electrostatics, J. Phys. Chem. , 100, 1578-1599 (1996)

M. Schaefer, C. Bartels and M. Karplus, Solution Conformations and Thermodynamics of Structured Peptides: Molecular Dynamics Simulation with an Implicit Solvation Model, J. Mol. Biol. , 284, 835-848 (1998)

SUPERPOSITION OF COORDINATE SETS

S. J. Kearsley, An Algorithm for the Simultaneous Superposition of a Structural Series, J. Comput. Chem. , 11, 1187-1192 (1990)

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A. D. McLachlan, Rapid Comparison of Protein Structures, Acta Cryst. , A38, 871-873 (1982)

S. C. Nyburg, Some Uses of a Best Molecular Fit Routine, Acta Cryst. , B30, 251-253 (1974)

LOCATION OF TRANSITION STATES

R. Czerminski and R. Elber, Reaction Path Study of Conformational Transitions and Helix Formation in a Tetrapeptide, Proc. Nat. Acad. Sci. USA , 86, 6963 (1989)

R. S. Berry, H. L. Davis and T. L. Beck, Finding Saddles on Multidimensional Potential Surfaces, Chem. Phys. Lett. , 147, 13 (1988)

K. Muller, Reaction Paths on Multidimensional Energy Hypersurfaces, Ang. Chem. Int. Ed. Engl., 19, 1-13 (1980)

S. Bell and J. S. Crighton, Locating Transition States, J. Chem. Phys. , 80, 2464-2475 (1984)

S. Fischer and M. Karplus, Conjugate Peak Refinement: An Algorithm for Finding Reaction Paths and Accurate Transition States in Systems with Many Degrees of Freedom, Chem. Phys. Lett. , 194, 252-261 (1992)

J. E. Sinclair and R. Fletcher, A New Method of Saddle-Point Location for the Calculation of Defect Migration Energies, J. Phys. C , 7, 864-870 (1974)

R. Elber and M. Karplus, A Method for Determining Reaction Paths in Large Molecules: Application to Myoglobin, Chem. Phys. Lett. , 139, 375-380 (1987)

D. T. Nguyen and D. A. Case, On Finding Stationary States on Large-Molecule Potential Energy Surfaces, J. Phys. Chem. , 89, 4020-4026 (1985)

T. A. Halgren and W. N. Lipscomb, The Synchronous-Transit Method for Determining Reaction Pathways and Locating Molecular Transition States, Chem. Phys. Lett. , 49, 225- 232 (1977)

G. T. Barkema and N. Mousseau, Event-Based Relaxation of Continuous Disordered Systems, Phys. Rev. Lett. , 77, 4358-4361 (1996)




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department of chemistry University of Cambridge