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Determination, Prediction, And Understanding Of Structures, Using The Energy Landscapes Of Chemical Systems – Part II

J. C. Schön, M. Jansen
Published 2001 · Chemistry

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Abstract In the past decade, new theoretical approaches have been developed to determine, predict and understand the struc-ture of chemical compounds. The central element of these methods has been the investigation of the energy landscape of chemical systems. Applications range from extended crystalline and amorphous compounds over clusters and molecular crystals to proteins. In this review, we are going to give an introduction to energy landscapes and methods for their investigation, together with a number of examples. These include structure prediction of extended and mo-lecular crystals, structure prediction and folding of proteins, structure analysis of zeolites, and structure determination of crystals from powder diffraction data.
This paper references
10.1006/JSSC.1997.7688
Determination of Structure Candidates of Simple CrystallineAB2Systems
M. Wevers (1998)
10.1007/978-3-322-86415-4_1
Wege zu Festkörpern jenseits der thermodynamischen Stabilität
M. Jansen (1996)
10.1063/1.461157
Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
A. Roitberg (1991)
10.1002/JCC.540040211
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks (1983)
10.1016/0263-7855(94)80069-3
GroupBuild: a fragment-based method for de novo drug design
Sergio H. Rotstein (1994)
10.1002/PROT.340230111
Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
J. M. Troyer (1995)
10.1021/JP970984N
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
D. Wales (1997)
10.1021/JP970908K
The energy landscape of myoglobin : An optical study
D. T. Leeson (1997)
10.1073/PNAS.95.10.5545
On the thermodynamic hypothesis of protein folding.
S. Govindarajan (1998)
10.1002/PROT.340040106
Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system
P. Dauber-Osguthorpe (1988)
10.1021/JA9621760
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
W. Jorgensen (1996)
10.1088/0953-8984/8/2/004
Studying the energy hypersurface of continuous systems - the threshold algorithm
J. C. Schön (1996)
10.1063/1.473299
The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
O. Becker (1997)
10.1126/SCIENCE.287.5458.1615
The catalytic pathway of cytochrome p450cam at atomic resolution.
I. Schlichting (2000)
10.1143/PTPS.138.394
The Multicanonical Weighted Histogram Analysis Method for the Free Energy Landscape along Structural Transition Paths
S. Ono (2000)
10.1524/ZKRI.1997.212.11.768
Enumeration of periodic tetrahedral frameworks
M. Treacy (1997)
10.1002/JCC.540120510
Geometry optimization in cartesian coordinates: The end of the Z‐matrix?
J. Baker (1991)
10.1039/FT9938901305
Locating stationary points for clusters in cartesian coordinates
D. Wales (1993)
10.1103/PHYSREVLETT.81.1126
Effect of Conformational Constraints on the Topography of Complex Potential Energy Surfaces
Y. Levy (1998)
10.1016/S0022-3093(98)00637-1
The glass transition: general scenario and crossover temperature
A. Sokolov (1998)
10.1002/PRO.5560020915
Modeling of protein loops by simulated annealing
V. Collura (1993)
10.1103/PHYSREVB.53.13857
Energy minimization using the classical density distribution: Application to sodium chloride clusters.
Amara (1996)
10.1110/PS.8.8.1591
Distinguishing between sequential and nonsequentially folded proteins: Implications for folding and misfolding
C. Tsai (1999)
10.1002/9780470110560.CH1
Theoretical and empirical approaches to protein-structure prediction and analysis.
G. Maggiora (1991)
10.1142/9789812839664_0001
Barrier crossings:. classical theory of rare but important events
David Chandler (1998)
10.1039/B002956O
Prediction of high pressure phases in the systems Li3N, Na3N, (Li, Na)3N, Li2S and Na2S
J. C. Schön (2001)
10.1103/PHYSREVLETT.75.164
Reptation, entropic trapping, percolation, and rouse dynamics of polymers in "random" environments.
Slater (1995)
Synthesis, structure and properties of Ag 2 PdO 2
M. Schreyer (2001)
10.1016/S1387-1811(98)00249-2
Ordered mesoporous materials
Ulrike Ciesla (1999)
10.1103/PHYSREVLETT.78.4051
Properties of a glass-forming system as derived from its potential energy landscape
A. Heuer (1997)
10.1002/(SICI)1097-0134(199702)27:2<213::AID-PROT8>3.0.CO;2-G
Geometric versus topological clustering: An insight into conformation mapping
O. Becker (1997)
Geochemische Verteilungsgesetze der Elemente
V. M. Goldschmidt (1923)
10.1021/JP9806258
SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics
T. Huber (1998)
Crystal Structure Solution from Powder Diffraction Data – State of the Art and Perspectives
A. Meden (1998)
10.1021/ci00002a004
The development of versions 3 and 4 of the Cambridge Structural Database System
F. Allen (1991)
10.1016/S0010-4655(99)00305-7
Understanding the glass transition and the amorphous state of matter: can computer simulation solve the challenge?
K. Binder (1999)
10.1002/ANIE.199612861
First Step Towards Planning of Syntheses in Solid‐State Chemistry: Determination of Promising Structure Candidates by Global Optimization
J. C. Schön (1996)
10.1007/BF00124016
Local elevation: A method for improving the searching properties of molecular dynamics simulation
T. Huber (1994)
10.1109/43.602476
An evaluation of parallel simulated annealing strategies with application to standard cell placement
J. Chandy (1997)
10.1016/S1387-1811(98)00245-5
Simulations of the non-framework cation configurations in dehydrated Na–Ca and Na–Li zeolite A
J. Lignières (1999)
10.1021/JM991040K
Ochratoxin binding to phenylalanyl-tRNA synthetase: computational approach to the mechanism of ochratoxicosis and its antagonism.
D. McMasters (1999)
10.1080/08893119508039920
Incommensurate crystal structures
S. V. Smaalen (1995)
10.1016/S0920-5861(98)00500-8
Predicting locations of non-framework species in zeolite materials
V. Guliants (1999)
10.1016/S1293-2558(00)01090-6
Synthesis of potassium cyanamide, and crystal structure determination by pareto optimisation of the cost functions ‘lattice energy’ and ‘powder intensities’
M. Becker (2000)
10.1038/183141A0
A Geometrical Approach to the Structure Of Liquids
J. Bernal (1959)
10.1016/0022-2836(78)90297-8
Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins.
J. Garnier (1978)
10.1002/JCC.540110115
Protein structure prediction using a combination of sequence homology and global energy minimization I. Global energy minimization of surface loops
Michael J. Dudek (1990)
10.1038/342260A0
Determination of 4-connected framework crystal structures by simulated annealing
M. Deem (1989)
10.1063/1.478992
Principal coordinate analysis on a protein model
Nuran Elmaci (1999)
10.1051/JPHYS:019880049090148500
On lumped models for thermodynamic properties of simulated annealing problems
B. Andresen (1988)
10.1016/S1359-0278(96)00028-4
Update on protein structure prediction: results of the 1995 IRBM workshop.
T. Hubbard (1996)
10.1107/S0108767381089411
INORGANIC CRYSTAL STRUCTURE DATABASE
G. Bergerhoff (1981)
10.1039/A901227C
The prediction of inorganic crystal structures using a genetic algorithm and energy minimisation
S. Woodley (1999)
10.1063/1.466098
Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: Application to enhanced equilibrium averaging and global optimization
Jianpeng Ma (1993)
10.1006/JCPH.1993.1010
New optimization heuristics
G. Dueck (1993)
10.1016/0021-9991(76)90078-4
Efficient estimation of free energy differences from Monte Carlo data
C. H. Bennett (1976)
Transferable ab Initio Intermolecular Potentials
W.T.M. Mooij (1999)
10.1021/BI00699A002
Prediction of protein conformation.
P. Chou (1974)
10.2174/0929867003374534
Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach.
G. Müller (2000)
10.1063/1.472836
A thermodynamic distance criterion of optimality for the calculation of free energy changes from computer simulations
J. C. Schön (1996)
10.1002/BBPC.19940981207
Determination of candidate structures for Lennard‐Jones‐crystals through cell optimisation
J. C. Schön (1994)
10.1063/1.457790
Exploring potential energy surfaces with transition state calculations
H. Davis (1990)
10.1002/BBPC.199500047
Strukturvorhersage von Kristallen aus binären Edelgasgemischen mit globalen und lokalen Optimierungsmethoden
H. Putz (1995)
10.1103/PHYSREVB.61.1681
Optical characterization of indium-terminated GaAs(001) surfaces
C. Goletti (2000)
Energy Parameters in Polypeptides
G. Nemethy (1996)
10.1002/BBPC.19961000903
Studying the energy hypersurface of multi‐minima systems — the threshold and the lid algorithm
J. C. Schön (1996)
10.1073/PNAS.95.6.2932
Self-consistently optimized energy functions for protein structure prediction by molecular dynamics.
K. Koretke (1998)
10.1021/MA00050A046
EVIDENCE FOR ENTROPIC BARRIER TRANSPORT OF LINEAR, STAR, AND RING MACROMOLECULES IN ELECTROPHORESIS GELS
D. Hoagland (1992)
10.1002/(SICI)1096-987X(19980415)19:5<548::AID-JCC7>3.0.CO;2-M
Protein structure prediction using a combination of sequence homology and global energy minimization: II. Energy functions
Michael J. Dudek (1998)
10.1016/B978-012164135-1/50007-1
6 – Reverse Monte Carlo Methods for Structural Modelling
R. Mcgreevy (1997)
10.1016/S0921-4526(98)01473-2
Spin-glass approach to low-temperature anomalies in glasses
U. Horstmann (1999)
10.1287/INTE.20.4.74
Tabu Search: A Tutorial
F. Glover (1990)
10.1006/JTBI.2000.1097
Transition-state ensemble in enzyme catalysis: possibility, reality, or necessity?
B. Ma (2000)
10.1021/JA963689+
SMOG : DE NOVO DESIGN METHOD BASED ON SIMPLE, FAST, AND ACCURATE FREE ENERGY ESTIMATES. 2. CASE STUDIES IN MOLECULAR DESIGN
R. S. DeWitte (1997)
10.1016/S1359-0278(97)00011-4
Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996.
Roland L. Dunbrack (1997)
10.1016/S0009-2614(99)01366-4
Definition of a `guiding function' in global optimization: a hybrid approach combining energy and R-factor in structure solution from powder diffraction data
Oliver J. Lanning (2000)
Simulated Annealing , MATCH – Comm
V. Kvasnicka (1998)
10.1007/978-3-642-96483-1
Monte Carlo Methods in Statistical Physics
M. Newman (1999)
10.1051/JCP/1968650044
Are there pathways for protein folding
C. Levinthal (1968)
10.1103/PHYSREVE.51.R1
Traveling salesman problem and Tsallis statistics.
Penna (1995)
10.2307/3008501
Optimization Theory with Applications
D. A. Pierre (1986)
10.1103/PHYSREVB.51.1447
Ab initio total-energy pseudopotential calculations for polymorphic B2O3 crystals.
Takada (1995)
10.1002/9780470122921.CH2
Prediction of the secondary structure of proteins from their amino acid sequence.
P. Y. Chou (1978)
10.1063/1.477521
Realistic master equation modeling of relaxation on complete potential energy surfaces: Kinetic results
K. Ball (1998)
10.1021/J100194A068
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
G. Némethy (1994)
10.1021/JA9929990
Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions†
J. Pillardy (2000)
10.1039/JM9940400831
Self-consistent interatomic potentials for the simulation of binary and ternary oxides
Timothy S. Bush (1994)
10.1107/S0021889869006558
A profile refinement method for nuclear and magnetic structures
H. M. Rietveld (1969)
10.1063/1.1749657
Statistical Mechanics of Fluid Mixtures
J. Kirkwood (1935)
10.1103/PhysRevLett.83.2210
COMPUTER INVESTIGATION OF THE ENERGY LANDSCAPE OF AMORPHOUS SILICA
P. Jund (1999)
10.1002/(SICI)1097-0134(199601)24:1<18::AID-PROT2>3.0.CO;2-K
Secondary structure prediction and unrefined tertiary structure prediction for cyclin A, B, and D
D. Gerloff (1996)
Structure Prediction and Modelling of Solids: An Energy Landscape Point of View
J. C. Schön (1998)
Crystal Structures from Building Blocks: The Metallates
H. Eschrig (1999)
10.1016/S0959-440X(97)80055-3
Progress in protein structure prediction.
D. Jones (1997)
10.1002/PRO.5560070916
Distance geometry generates native‐like folds for small helical proteins using the consensus distances of predicted protein structures
Enoch S. Huang (1998)
10.1002/(SICI)1097-0134(19991201)37:4<592::AID-PROT10>3.0.CO;2-2
A method for the improvement of threading‐based protein models
A. Kolinski (1999)
10.1103/PHYSREVB.55.12011
Ab initio solution of a complex crystal structure from powder-diffraction data using simulated-annealing method and a high degree of molecular flexibility
Yuri G. Andreev (1997)
10.1063/1.480863
Shear-induced changes of the potential energy landscape underlying n-butane liquids and glasses
M. M. Frey (2000)
10.1063/1.479861
THE APPLICATION OF THE ENERGY LANDSCAPE MODEL TO POLYMERS
C. Roland (1999)
10.1016/S0014-5793(98)00988-0
The M2 channel of influenza A virus: a molecular dynamics study
Q. Zhong (1998)
10.1107/S0108768199001202
Modelling the crystal structure of the 2-hydronitronylnitroxide radical (HNN): observed and computer-generated polymorphs.
Filippini (1999)
10.1093/PROTEIN/9.6.485
A molecular dynamics study of the effect of carbon tetrachloride on enzyme structure and dynamics: subtilisin.
Y. Zheng (1996)
10.1002/(SICI)1097-0134(199607)25:3<342::AID-PROT6>3.3.CO;2-3
Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes.
Gennady M Verkhivker (1996)
Crystal Structure versus Molecular Structure: New Developments
G. Filippini (1992)
10.1002/(SICI)1097-0134(19981115)33:3<408::AID-PROT9>3.0.CO;2-2
Folding‐unfolding energy change of a simple sphere model protein and an energy landscape of the folding process
Y. Fukunishi (1998)
10.1016/0927-0256(95)00016-J
Determination of candidate structures for simple ionic compounds through cell optimisation
J. C. Schön (1995)
10.1146/ANNUREV.BIOPHYS.29.1.411
A decade of CLC chloride channels: structure, mechanism, and many unsettled questions.
M. Maduke (2000)
10.1016/0022-2836(92)90230-H
Prediction of protein folding pathways.
G. Chelvanayagam (1992)
10.1088/0953-8984/11/33/316
Global aspects of the energy landscape of metastable crystal structures in ionic compounds
M. A. C. Wevers (1999)
10.1006/JMBI.1997.0959
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
K. Simons (1997)
10.1007/BF00141573
GenStar: A method for de novo drug design
S. H. Rotstein (1993)
10.1073/PNAS.89.19.9029
Protein tertiary structure recognition using optimized Hamiltonians with local interactions.
R. A. Goldstein (1992)
10.1103/PHYSREVA.39.5350
Electrostatic interactions in periodic Coulomb and dipolar systems.
Cichocki (1989)
10.1146/ANNUREV.BIOPHYS.29.1.291
Comparative protein structure modeling of genes and genomes.
M. A. Martí-Renom (2000)
10.1016/0009-2614(94)00754-3
Protein simulation below the glass-transition temperature. Dependence on cooling protocol
P. J. Steinbach (1994)
Tertiary structure prediction of mixed alpha/beta proteins via energy minimization.
D. Standley (1998)
10.1103/REVMODPHYS.72.259
Heteropolymer freezing and design: Towards physical models of protein folding
V. Pande (2000)
10.1002/PRO.5560040401
Principles of protein folding — A perspective from simple exact models
Ken A. Dill (1995)
10.1063/1.478496
Levitation effect and its relationship with the underlying potential energy landscape
Chitra Rajappa (1999)
Klassische Mechanik, Akad. Verlagges
H. Goldstein (1978)
10.1021/JP991641N
Transferable ab Initio Intermolecular Potentials. 1. Derivation from Methanol Dimer and Trimer Calculations
F. B. Duijneveldt (1999)
10.1038/31146
Hard sell for the Sun
G. A. Gellert (1998)
De novo design of structure-directing agents for the synthesis of microporous
D. W. Lewis (1996)
10.1021/JA00044A035
Framework crystal structure solution by simulated annealing : test application to known zeolite structures
M. Deem (1992)
10.1016/0022-2836(92)90936-E
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins.
R. Abagyan (1992)
10.1088/0953-8984/11/10A/003
Monte Carlo and molecular dynamics simulation of the glass transition of polymers
K. Binder (1998)
10.1209/0295-5075/7/6/001
Fuzzy Logic, m-Spin Glasses and 3-SAT
H. Müller‐Krumbhaar (1988)
10.1103/PhysRevLett.84.386
Mean-field HP model, designability and alpha-helices in protein structures.
C. Shih (2000)
10.1021/JP991384M
The equation of state of an energy landscape
P. Debenedetti (1999)
10.1214/AOMS/1177697196
A Maximization Technique Occurring in the Statistical Analysis of Probabilistic Functions of Markov Chains
L. E. Baum (1970)
10.1002/1521-3773(20000703)39:13<2270::AID-ANIE2270>3.0.CO;2-A
De Novo Prediction of Inorganic Structures Developed through Automated Assembly of Secondary Building Units (AASBU Method)
C. M. Draznieks (2000)
10.1063/1.477520
Realistic master equation modeling of relaxation on complete potential energy surfaces: Partition function models and equilibrium results
K. Ball (1998)
10.1038/383239A0
Entropic control of particle motion using passive surface microstructures
A. Dinsmore (1996)
10.1524/zkri.1999.214.9.506
An introduction to Computational crystallography
B. Winkler (1999)
10.1016/s1369-7021(04)00294-9
Quantum theory of the solid state
J. Callaway (1974)
10.1524/ZKRI.1957.109.1-6.475
Einführung in die Kristallographie
G. Menzer (1957)
10.1002/CHIN.199940007
Li4SeO5, the First Orthoselenate, Crystallizes as an Order Variant of a Theoretically Predicted A[5]B[5] Structure Type.
H. Haas (1999)
10.1080/13642819908223084
Transitions between metastable states in silica clusters
Claudio Brangian (1999)
10.1007/BF02683451
The top quark
M. L. Mangano (2000)
10.1103/PhysRevE.61.1681
Potential energy landscape and long-time dynamics in a simple model glass
Angelani (2000)
10.1016/0021-9991(90)90201-B
Threshold accepting: a general purpose optimization algorithm appearing superior to simulated anneal
G. W. Dueck (1990)
10.1021/JA00092A006
Multiple Highly Diverse Structures Complementary to Enzyme Binding Sites: Results of Extensive Application of a de Novo Design Method Incorporating Combinatorial Growth
R. Bohacek (1994)
10.1006/JSSC.1996.0369
The Computational Investigation of the Phase Transition from the GeO2α-Quartz Structure to the Rutile Structure
A. George (1996)
10.1016/S0960-9822(99)80130-4
Structure prediction: The state of the art
D. Shortle (1999)
10.1126/SCIENCE.1716375
The combination of symbolic and numerical computation for three-dimensional modeling of RNA.
F. Major (1991)
Protein structure prediction by threading: force field philosophy,
T. Huber (2001)
10.1007/BF00124349
CAVEAT: A program to facilitate the design of organic molecules
Georges Lauri (1994)
10.1073/PNAS.96.10.5482
Protein structure prediction by global optimization of a potential energy function.
A. Liwo (1999)
10.1093/PROTEIN/13.7.453
Constructing side chains on near-native main chains for ab initio protein structure prediction.
R. Samudrala (2000)
10.1051/JP1:1991146
Ensemble approach to simulated annealing
G. Ruppeiner (1991)
10.1006/JMBI.2000.3835
Ab initio construction of protein tertiary structures using a hierarchical approach.
Y. Xia (2000)
10.1021/JA993119K
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1
C. Simmerling (2000)
10.1016/S0098-1354(00)00461-0
Deterministic global optimization and torsion angle dynamics for molecular structure prediction
J. L. Klepeis (2000)
10.1103/PHYSREVLETT.71.211
New Monte Carlo algorithm: Entropic sampling.
Lee (1993)
10.1063/1.444225
Time‐dependent self‐consistent field approximation for intramolecular energy transfer. I. Formulation and application to dissociation of van der Waals molecules
R. Gerber (1982)
10.1088/0305-4470/34/19/306
Characteristic regions on the energy landscape of MgF2
M. Wevers (2001)
10.1107/S0108767390004512
Space‐group frequencies of proteins and of organic compounds with more than one formula unit in the asymmetric unit
N. Padmaja (1990)
10.1016/S0378-4371(99)00259-9
POTENTIAL ENERGY LANDSCAPE SIGNATURES OF SLOW DYNAMICS IN GLASS FORMING LIQUIDS
S. Sastry (1999)
10.1021/CR00023A003
POTENTIAL SURFACES AND DYNAMICS : WHAT CLUSTERS TELL US
R. Berry (1993)
10.1002/(SICI)1521-3773(19981002)37:18<2527::AID-ANIE2527>3.0.CO;2-#
Silicon Boron Nitrides: Hypothetical Polymorphs of Si3 B3 N7.
P. Kroll (1998)
10.1016/0009-2614(96)00255-2
A gradient-only algorithm for tracing a reaction path uphill to the saddle of a potential energy surface
W. Quapp (1996)
10.1016/S0959-440X(00)00062-2
Long timescale simulations.
V. Daggett (2000)
Genetic Algorithms and Simulated Annealing
Lawrence Davis (1987)
Theoretical and Empirical Approaches to Protein-Structure Prediction and Analysis. In: Methods of Biochemical Analysis, Volume 35: Protein Structure Determination
G. M. Maggiora (1991)
10.1107/S0021889899006615
Combined method for ab initio structure solution from powder diffraction data
H. Putz (1999)
10.1007/978-3-662-08994-1_14
Multi-basin dynamics of a protein in aqueous solution
A. García (1995)
10.1016/S0009-2614(97)01222-0
Multi-dimensional entropy sampling Monte Carlo method and free energy landscape of Ar13
G. Chen (1997)
One nanosecond molecular dynamics simulation of the N-terminal domain of the lambda repressor protein.
D. Kombo (2000)
10.1088/0305-4470/30/16/006
Temperature evolution and bifurcations of metastable states in mean-field spin glasses, with connections with structural glasses
A. Barrat (1997)
10.1007/BF02456786
Statistical mechanics on the space of kinetic folding pathways
A. Fernández (1995)
10.1016/S0959-440X(00)00073-7
Structures of virus and virus-like particles.
J. Johnson (2000)
10.1021/JP972424U
Diffusion Equation and Distance Scaling Methods of Global Optimization: Applications to Crystal Structure Prediction
R. Wawak (1998)
10.1016/S0927-796X(99)00005-4
The future of atomic resolution electron microscopy for materials science
J. Spence (1999)
10.1039/A801266K
Sampling ensembles of deterministic transition pathways
P. Bolhuis (1998)
10.1007/BF02337561
The importance of short structural motifs in protein structure analysis
R. Unger (1993)
10.1063/1.480217
Evolution of the Potential Energy Surface with Size for Lennard-Jones Clusters
J. Doye (1999)
10.1088/0305-4470/20/5/032
Criteria for an optimum simulated annealing schedule for problems of the travelling salesman type
S. Rees (1987)
10.1107/S0108767399000197
Reverse Monte Carlo modelling of neutron powder diffraction data.
Mellergård (1999)
10.1016/S0163-7258(99)00031-5
Computational approaches to structure-based ligand design.
D. Joseph-McCarthy (1999)
10.1051/RO/1998320100431
Simulated annealing algorithm : technical improvements
D. Delamarre (1998)
10.1016/S0959-440X(99)80025-6
New Monte Carlo algorithms for protein folding.
U. H. Hansmann (1999)
10.1089/cmb.1997.4.217
Current Limitations to Protein Threading Approaches
T. Smith (1997)
Adaptation in natural and artificial systems
J. Holland (1975)
10.1146/ANNUREV.BI.47.070178.001343
Empirical predictions of protein conformation.
P. Chou (1978)
10.1107/S0108768191007255
Crystallochemical model and prediction for zeolite-type structures
N. Engel (1991)
10.1039/A707351H
Inclusion of symmetry for the enhanced determination of crystalline structures from powder diffraction data using simulated annealing
L. Reinaudi (1998)
10.1287/MOOR.13.2.311
Cooling Schedules for Optimal Annealing
B. Hajek (1988)
10.1006/JCPH.1999.6218
Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations
J. Gullingsrud (1999)
10.1089/106652799318346
Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes
J. Kleinberg (1999)
10.1088/0953-8984/11/10A/005
Simple glass-forming liquids: their definition, fragilities, and landscape excitation profiles
C. Angell (1999)
10.1002/(SICI)1521-3773(19990712)38:13/14<1909::AID-ANIE1909>3.0.CO;2-#
Li4SeO5, the First Orthoselenate, Crystallizes as an Order Variant of a Theoretically Predicted A[5]B[5] Structure Type
H. Haas (1999)
10.1016/S0958-1669(96)80118-2
The current state of the art in protein structure prediction.
J. Moult (1996)
10.1021/JP9920949
Dimensional Strategies and the Minimization Problem: Barrier-Avoiding Algorithms
D. Faken (1999)
10.1016/S0959-440X(00)00063-4
Effective energy functions for protein structure prediction.
T. Lazaridis (2000)
10.1016/0003-2697(84)90583-9
Proteins: Structures and Molecular Properties
Thomas E. Creighton (1986)
10.1016/S0166-1280(97)00080-8
Quantitative visualization of a macromolecular potential energy “funnel”
O. Becker (1997)
10.1007/s100510050537
Statistical mechanics of warm and cold unfolding in proteins
A. Hansen (1998)
10.1007/978-3-642-93499-5
Properties of Chemically Interesting Potential Energy Surfaces
D. Heidrich (1991)
10.1002/(SICI)1097-0134(19990901)36:4<454::AID-PROT9>3.0.CO;2-B
Protein fold recognition score functions: Unusual construction strategies
D. Ayers (1999)
10.1021/J100079A005
Clusters: Tools for Studying Potential Surfaces and Their Connection to Molecular Dynamics
R. Berry (1994)
10.1103/PHYSREVLETT.83.1688
ENTROPIC TRAPPING AND ESCAPE OF LONG DNA MOLECULES AT SUBMICRON SIZE CONSTRICTION
J. Han (1999)
10.1002/(SICI)1097-0134(19980701)32:1<52::AID-PROT7>3.0.CO;2-G
Testing a new Monte Carlo algorithm for protein folding
U. Bastolla (1998)
10.1016/0022-3093(91)90664-R
Entropic barrier model for polymer diffusion in concentrated polymer solutions and random media
M. Muthukumar (1991)
10.1063/1.1699114
Equation of state calculations by fast computing machines
N. Metropolis (1953)
10.1021/MA00032A015
Entropy-induced frozen morphology in unstable polymer blends
M. Kotnis (1992)
Combinatorial Materials Science and Cataly
B. Jandeleit (1986)
10.1021/BI961875M
Catalysis by entropic guidance from enzymes.
L. Young (1996)
10.1103/PHYSREVA.25.978
Hidden structure in liquids
F. H. Stillinger (1982)
10.1007/BF00126217
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
Hans-Joachim Böhm (1992)
10.1103/PHYSREVLETT.65.3301
Direct dynamical calculation of entropy and free energy by adiabatic switching.
Watanabe (1990)
10.1006/JMBI.1999.3006
Protein folding: from the levinthal paradox to structure prediction.
B. Honig (1999)
10.1006/JMBI.2000.3714
De novo determination of protein structure by NMR using orientational and long-range order restraints.
J. C. Hus (2000)
10.1107/S0021889898015763
Determination of symmetries and idealized cell parameters for simulated structures
R. Hundt (1999)
10.1093/PROTEIN/4.4.443
Adaptability of restrained molecular dynamics for tertiary structure prediction: application to Crotalus atrox venom phospholipase A2.
T. Fujiyoshi‐yoneda (1991)
10.1016/0960-9822(93)90348-R
A method for predicting protein structure from sequence
J. Skolnick (1993)
10.1103/PhysRevLett.84.2168
Metastable states as a key to the dynamics of supercooled liquids
F Buchner (2000)
10.1093/PROTEIN/4.3.271
A predicted three-dimensional structure of human cytochrome P450: implications for substrate specificity.
M. Zvelebil (1991)
10.1002/(SICI)1097-0282(199606)38:6<769::AID-BIP8>3.0.CO;2-P
RNA loop structure prediction via bond scaling and relaxation.
T. Frederic (1996)
10.1073/PNAS.30.9.244
The Compressibility of Media under Extreme Pressures.
F. D. Murnaghan (1944)
10.1107/S0108767396000967
Crystallography of quasiperiodic crystals
A. Yamamoto (1996)
10.1073/PNAS.160271197
Statistical significance of protein structure prediction by threading.
L. Mirny (2000)
10.1073/PNAS.95.17.9897
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation.
Y. Duan (1998)
10.1073/PNAS.87.16.6388
Origins of structure in globular proteins.
H. S. Chan (1990)
10.1107/S002188980000248X
Whole-profile structure solution from powder diffraction data using simulated annealing
A. A. Coelho (2000)
10.1073/PNAS.92.20.9029
Kinetic traps in lysozyme folding.
T. Kiefhaber (1995)
ESPOIR : A Program for Solving Structures by Monte Carlo from Powder Diffraction Data
A. Bail (2000)
10.1016/S0959-440X(99)80044-X
Structure, folding and catalysis of the small nucleolytic ribozymes.
D. Lilley (1999)
10.1002/(SICI)1097-0134(199702)27:2<290::AID-PROT14>3.0.CO;2-H
A method for the prediction of surface “U”‐turns and transglobular connections in small proteins
A. Kolinski (1997)
10.1016/S1380-7323(99)80006-5
Predicting structures of compounds in the solid state by the global optimisation approach
J. C. Schön (1999)
10.1103/PHYSREV.168.1068
Atomic Arrangement in Vitreous Selenium
R. Kaplow (1968)
10.1038/NSB1095-848
Looking into the energy landscape of myoglobin
D. T. Leeson (1995)
10.1007/BF00940812
Thermodynamical approach to the traveling salesman problem: An efficient simulation algorithm
V. Cerny (1985)
10.1016/S0378-4371(98)00263-5
Local state space geometry and thermal relaxation in complex landscapes: the spin-glass case
P. Sibani (1998)
10.1002/(SICI)1097-0282(200006)53:7<596::AID-BIP6>3.0.CO;2-U
One nanosecond molecular dynamics simulation of the N‐terminal domain of the λ repressor protein
D. Kombo (2000)
10.1021/J100055A032
Molecular mechanics potential for silica and zeolite catalysts based on ab initio calculations. 1. Dense and microporous silica
J. R. Hill (1994)
10.1002/(SICI)1096-987X(199906)20:8<799::AID-JCC6>3.0.CO;2-Z
Upack program package for crystal structure prediction: Force fields and crystal structure generation for small carbohydrate molecules
B. van Eijck (1999)
10.1016/S0959-440X(99)80051-7
From protein structure to function.
C. Orengo (1999)
10.1107/S0108767398007363
Advances in Powder Diffraction Analysis
D. Louër (1998)
10.1002/(SICI)1096-987X(20000130)21:2%3C147::AID-JCC6%3E3.0.CO;2-6
A parallel tabu search for conformational energy optimization of oligopeptides
Luis B. Morales (2000)
10.1063/1.445869
Comparison of simple potential functions for simulating liquid water
W. Jorgensen (1983)
10.1080/13642819908223083
Energy and entropy barriers of two-level systems in argon clusters: an energy landscape approach
O. Pilla (1999)
10.1039/A606455H
GULP: A computer program for the symmetry-adapted simulation of solids
J. Gale (1997)
10.1088/0953-8984/10/27/013
Coarse graining of a spin-glass state space
T. H. Klotz (1998)
10.1073/PNAS.93.5.1743
Theoretical prediction of a crystal structure.
R. Wawak (1996)
Can we predict crystal structures of minerals? Nova
W. H. Baur (1999)
10.1016/0022-4596(91)90375-R
Divalent metal halide double salts in equilibrium with their aqueous solutions: II. Factors determining their crystal structures
I. Brown (1991)
10.1093/nar/28.1.45
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
A. Bairoch (2000)
10.1021/MA980702X
Lattice Cluster Theory for Pedestrians: The Incompressible Limit and the Miscibility of Polyolefin Blends
K. Freed (1998)
10.1088/0965-0393/7/6/309
A constitutive model for physical ageing in amorphous glassy polymers
A. Drozdov (1999)
10.1209/0295-5075/22/7/001
Emergent Hierarchical Structures in Complex-System Dynamics.
P. Sibani (1993)
Handbook of Interatomic Potentials III
V. Torres (1987)
10.1016/S0301-0104(98)00414-5
Locating critical points on multi-dimensional surfaces by genetic algorithm: test cases including normal and perturbed argon clusters
P. Chaudhury (1999)
10.1021/JA00124A002
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell (1995)
Transferable ab Initio Intermolecular Potentials
W.T.M. Mooij (1999)
Are there pathways for protein
C. Levinthal (1968)
Energy Parameters in Polypeptides
N. Nemethy (1983)
10.1515/REVCE.2000.16.2.71
Modeling of Diffusion in Zeolites
F. Keil (2000)
10.1063/1.480011
Energy Landscape of a Model Protein
M. Miller (1999)
10.1038/NSB0398-236
A metastable state in folding simulations of a protein model
A. Dinner (1998)
Investigating the energy landscape of continuous systems – the threshold algorithm
J. C. Schön (1996)
Strukturvorhersage in gemischten Edelgaskristallen durch globale Optimierung
H. Putz (1995)
10.1039/JM9940400781
Computer modelling as a technique in materials chemistry
C. Catlow (1994)
10.1002/(SICI)1097-461X(2000)77:1<90::AID-QUA10>3.0.CO;2-L
Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
J. Lee (2000)
10.1016/S0010-4655(98)00176-3
The lid method for exhaustive exploration of metastable states of complex systems
P. Sibani (1999)
10.1002/PRO.5560050607
Self‐consistently optimized statistical mechanical energy functions for sequence structure alignment
K. Koretke (1996)
10.1088/0953-8984/7/46/003
Computer modelling of B2O3. I. New interatomic potentials, crystalline phases and predicted polymorphs
A. Takada (1995)
10.1002/jcc.540070216
An all atom force field for simulations of proteins and nucleic acids
S. Weiner (1986)
10.1107/S0108768194009651
Attempted prediction of the crystal structures of six monosaccharides
B. P. V. Eijck (1995)
10.1021/J100234A011
Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
G. Némethy (1983)
10.1063/1.2810459
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
C. L. Brooks (1988)
10.1006/JSSC.2000.8902
Reversible Antifluorite to Anticotunnite Phase Transition in Li2S at High Pressures
Andrzej Grzechnik (2000)
10.1093/BIOMET/53.3-4.325
Some distance properties of latent root and vector methods used in multivariate analysis
J. Gower (1966)
10.1002/jcc.540141110
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problem
U. H. Hansmann (1993)
10.1063/1.479474
Dynamics on statistical samples of potential energy surfaces
K. Ball (1999)
10.1063/1.460250
ENERGY EQUIPARTITIONING IN THE CLASSICAL TIME-DEPENDENT HARTREE APPROXIMATION
J. Straub (1991)
10.1038/346343A0
Prediction of crystal structures from crystal chemistry rules by simulated annealing
J. Pannetier (1990)
10.1107/S0021889896000271
Early finding of preferred orientation : Applications to direct methods
A. Altomare (1996)
10.1103/PhysRevLett.83.3214
Inherent Structure Entropy of Supercooled Liquids
F. Sciortino (1999)
10.1103/PhysRevB.60.3200
Energy landscape, two-level systems and entropy barriers in Lennard-Jones clusters
G.Daldoss (1998)
10.1002/(SICI)1097-0134(19990601)35:4<408::AID-PROT4>3.0.CO;2-A
Estimating the total number of protein folds
S. Govindarajan (1999)
10.1051/JPHYS:019870048080125500
Zero-temperature scaling and simulated annealing
R. Ettelaie (1987)
10.1093/PROTEIN/12.12.1063
Hidden Markov model approach for identifying the modular framework of the protein backbone.
A. Camproux (1999)
10.1089/cmb.1998.5.531
Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach
B. Reva (1998)
10.1007/978-3-662-03695-2_8
Microscopic View of the Low-Temperature Anomalies in Glasses
A. Heuer (1998)
Strukturvorhersage für Festkörper mit festen Baueinheiten
J. C. Schön (1999)
10.1016/S0958-1669(99)00037-3
Predicting protein three-dimensional structure.
J. Moult (1999)
Heteropolymer Freezing and Design : Towards Physical Models of Protein
FoldingVijay S. PandePhysics (2000)
10.1002/(SICI)1097-0282(19971005)42:4<427::AID-BIP6>3.0.CO;2-S
The foldability landscape of model proteins
S. Govindarajan (1997)
10.18388/ABP.1997_4393
High coordination lattice models of protein structure, dynamics and thermodynamics.
A. Kolinski (1997)
10.1088/0305-4470/30/7/018
PREFERENTIAL TRAPPING ON ENERGY LANDSCAPES IN REGIONS CONTAINING DEEP-LYING MINIMA : THE REASON FOR THE SUCCESS OF SIMULATED ANNEALING ?
J. C. Schön (1997)
10.1063/1.458435
Walking on potential energy surfaces
J. Nichols (1990)
10.1016/S0959-440X(99)80050-5
Progress in protein structure prediction: assessment of CASP3.
M. Sternberg (1999)
10.1021/J100023A036
MOLECULAR MECHANICS POTENTIAL FOR SILICA AND ZEOLITE CATALYSTS BASED ON AB INITIO CALCULATIONS 2
J. Hill (1995)
10.1103/REVMODPHYS.62.251
Reaction-rate theory: fifty years after Kramers
P. Hänggi (1990)
10.1002/PROT.340190305
HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
M. Eisen (1994)
10.1063/1.475642
Atomic clusters and nanoscale particles: From coarse-grained dynamics to optimized annealing schedules
R. Kunz (1998)
10.1103/PHYSREVB.53.6165
Model interatomic potential for simulations in selenium.
Oligschleger (1996)
10.1088/0034-4885/55/3/001
Relaxation processes in supercooled liquids
W. Gotze (1992)
10.1021/ci970283n
Structure Prediction of Benzene Clusters Using a Genetic Algorithm
W. Pullan (1997)
Reversible Transitions in Na 2 S Under Pressure : A Comparison with the Cation Array in Na 2 SO 4
A. Vegas
Ab Initio Protein Folding- IS Conformational Space Searching Enough?
K. A. Olszewski (1998)
10.1016/S0081-1947(08)60337-9
Structure of Metallic Alloy Glasses
G. Cargill (1975)
10.1038/35004622
Ligand binding and conformational motions in myoglobin
A. Ostermann (2000)
10.1006/JMBI.1994.1220
Prediction of transmembrane segments in proteins utilising multiple sequence alignments.
B. Persson (1994)
10.1126/science.274.5292.1447b
Protein Structure Prediction
S. Benner (1996)
10.1023/A:1008311703619
Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: A simulation study
E. Eisenmesser (2000)
10.1016/S0010-4655(97)00117-3
Density-functional theory calculations for poly-atomic systems: electronic structure, static and elastic properties and ab initio molecular dynamics
M. Bockstedte (1997)
10.1021/JA993945T
Ab Initio Crystal Structure Predictions for Flexible Hydrogen-Bonded Molecules
W. T. Mooij (2000)
10.1007/s100510051140
Structurally constrained protein evolution: results from a lattice simulation
U. Bastolla (1999)
10.1002/(SICI)1097-0134(19990215)34:3<281::AID-PROT2>3.0.CO;2-2
Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides
C. Hardin (1999)
10.1063/1.478850
Locating all transition states and studying the reaction pathways of potential energy surfaces
K. Westerberg (1999)
10.1063/1.442352
ON FINDING TRANSITION STATES
C. J. Cerjan (1981)
10.1103/PHYSREVB.49.6667
Local phase-space structure and low-temperature dynamics of short-range Ising spin glasses.
Sibani (1994)
10.1107/S0108768100004584
A test of crystal structure prediction of small organic molecules.
J. Lommerse (2000)
10.1016/S0959-440X(96)80056-X
Hidden Markov models.
S. Eddy (1996)
10.1103/PHYSREVA.38.4261
Diffusion in hierarchies.
Hoffmann (1988)
10.1107/S0021889898008735
A New Algorithm for Space-Group Determination
A. Hannemann (1998)
10.1080/08927029508022340
Pressure and Temperature Dependence Study of the Denaturation of Ribonuclease A Solutions
J. Y. Yu (1995)
10.1016/S0031-8914(40)90098-2
Brownian motion in a field of force and the diffusion model of chemical reactions
H. Kramers (1940)
10.1002/CHIN.200043297
Crystallographic structure determination of unstable species.
I. Schlichting (2000)
10.1088/0034-4885/49/2/002
Models of the glass transition
J. Jäckle (1986)
10.1039/JM9930300531
Inorganic crystal structure prediction using simplified potentials and experimental unit cells: application to the polymorphs of titanium dioxide
C. Freeman (1993)
10.1002/PROT.340210302
Funnels, pathways, and the energy landscape of protein folding: A synthesis
J. D. Bryngelson (1995)
10.1006/JMRE.2000.2036
Three-dimensional solid-state NMR spectroscopy is essential for resolution of resonances from in-plane residues in uniformly (15)N-labeled helical membrane proteins in oriented lipid bilayers.
F. Marassi (2000)
10.1002/CHIN.199311299
Chemical and Steric Constraints in Inorganic Solids
I. Brown (1993)
10.1016/S0166-1280(98)00440-0
Kinetic consistency in the protein folding process
S. Saito (1999)
10.1002/JCC.540030404
Conformational analysis by energy embedding
G. Crippen (1982)
10.1021/JA00082A027
Peptide flexibility and calculations of an ensemble of molecules
D. Mierke (1994)
10.1021/JA00205A001
Molecular mechanics. The MM3 force field for hydrocarbons. 1
N. L. Allinger (1989)
10.1126/SCIENCE.285.5432.1368
Global optimization of clusters, crystals, and biomolecules.
D. Wales (1999)
10.1088/0953-8984/11/10/003
Computer Simulations of Supercooled Liquids and Glasses
W. Kob (1998)
10.1006/JMBI.1998.2092
Protein structure prediction by threading. Why it works and why it does not.
L. Mirny (1998)
10.1098/rspa.1980.0135
Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants
S. W. de Leeuw (1980)
Simulated Annealing, MATCH
V. Kvasnicka (1996)
10.1016/0009-2614(88)80215-X
Finding saddles on multidimensional potential surfaces
R. Berry (1988)
Energy Parameters in Polypeptides
F. A. Momany (1975)
10.1021/JM00145A002
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.
P. J. Goodford (1985)
10.1201/9780429499661
Introduction to the theory of neural computation
J. Hertz (1991)
10.1016/S0378-4371(96)00271-3
Generalized simulated annealing
C. Tsallis (1996)
Endeavour 1.0, CrystalImpact GbR
H. Putz (2000)
Broken ergodicity
R. Palmer (1982)
10.1103/PHYSREVB.41.10727
Structural properties and electronic structure of low-compressibility materials: beta -Si3N4 and hypothetical beta -C3N4.
Liu (1990)
10.1002/PROT.340110409
Computer design of bioactive molecules: A method for receptor‐based de novo ligand design
J. Moon (1991)
10.1063/1.1740409
High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
R. Zwanzig (1954)
10.1016/S0927-0256(98)00016-0
Investigation of the energy landscape of Mg2OF2
H. Putz (1998)
10.1002/(SICI)1521-3749(199910)625:10<1624::AID-ZAAC1624>3.0.CO;2-K
Structure Prediction for Crystalline Ca3SiBr2 using an Environment Dependent Potential
H. Putz (1999)
10.1006/JSSC.2000.8713
Ba3SiI2, a Double Salt of Barium Iodide and the Zintl Phase Ba2Si
S. Wengert (2000)
10.1103/PHYSREVLETT.55.2471
Unified approach for molecular dynamics and density-functional theory.
Car (1985)
10.1002/(SICI)1097-0134(199712)29:4<461::AID-PROT6>3.0.CO;2-B
Evolution of model proteins on a foldability landscape
S. Govindarajan (1997)
10.1006/JMBI.1996.0053
Global optimum protein threading with gapped alignment and empirical pair score functions.
R. Lathrop (1996)
10.1021/JP991640V
TRANSFERABLE AB INITIO INTERMOLECULAR POTENTIALS. 2. VALIDATION AND APPLICATION TO CRYSTAL STRUCTURE PREDICTION
W. T. Mooij (1999)
10.1209/epl/i2000-00134-y
Energy and entropy of metastable states in glassy systems
J. C. Schön (2000)
10.1002/CHIN.199808293
Computer Modeling as a Technique in Materials Chemistry
C. R. Catlow (1998)
10.1002/(SICI)1097-461X(1999)75:3<165::AID-QUA6>3.0.CO;2-Q
De Novo Predictions of the Quaternary Structure of Leucine Zippers and Other Coiled Coils
J. Skolnick (1999)
10.1016/0014-5793(93)80004-E
The nitrogenase MoFe protein
D. Gerloff (1993)
10.1006/JMBI.1993.1624
A structure refinement method based on molecular dynamics in four spatial dimensions.
R. V. van Schaik (1993)
10.1103/PhysRevE.57.2419
Traveling through potential energy landscapes of disordered materials: The activation-relaxation technique
N. Mousseau (1998)
10.1103/PHYSREVLETT.51.1127
Thermodynamic length and dissipated availability
P. Salamon (1983)
10.1103/PhysRevE.60.6507
Potential energy landscape of a model glass former: thermodynamics, anharmonicities, and finite size effects.
S. Büchner (1999)
10.1002/(SICI)1096-987X(199706)18:8%3C1036::AID-JCC7%3E3.0.CO;2-U
Fast clustering of equivalent structures in crystal structure prediction
B. P. V. Eijck (1997)
10.1021/JA01349A006
THE ATOMIC ARRANGEMENT IN GLASS
W. Zachariasen (1932)
10.1103/PHYSREVE.59.3207
Dependence of supercooled liquid dynamics on elevation in the energy landscape
T. Keyes (1999)
10.1146/ANNUREV.PHYSCHEM.48.1.545
Theory of protein folding: the energy landscape perspective.
J. Onuchic (1997)
10.1006/JMRE.2000.2037
Imaging membrane protein helical wheels.
J. Wang (2000)
10.1039/B002951N
Ab initio calculation of phase diagrams of ceramics and minerals
N. Allan (2001)
10.1016/0010-4655(88)90003-3
Simulated annealing with constant thermodynamic speed
P. Salamon (1988)
10.1002/1097-0134(20000815)40:3<343::AID-PROT10>3.0.CO;2-S
Protein threading using PROSPECT: Design and evaluation
Y. Xu (2000)
10.1016/S0959-440X(00)00067-1
Ab initio protein folding.
D. Osguthorpe (2000)
Structure prediction of solids via investigation of potential energy surfaces
J. C. Schön (1999)
Computer Simulation of the Structure and Properties of Oxides of M2O 2 SiO2 Type
D. K. Belashchenko (1994)
10.1016/S1089-3156(99)00026-4
Shear-induced disappearances of energy minima and plastic deformation in polymer glasses
D. Malandro (1999)
10.1063/1.473741
Exact enumeration of all conformations of a heteropolymer chain in a prescribed, non-compact volume
J. Mai (1997)
10.1093/PROTEIN/11.9.749
Optimizing potentials for the inverse protein folding problem.
T. Chiu (1998)
10.1063/1.477812
A biased Monte Carlo scheme for zeolite structure solution
M. Falcioni (1999)
10.1002/(SICI)1096-987X(19990415)20:5%3C546::AID-JCC6%3E3.0.CO;2-L
A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data
Y. Sun (1999)
10.1002/PROT.340230317
Evaluation of current techniques for Ab initio protein structure prediction
T. Defay (1995)
Vorhersage möglicher Kristallstrukturtypen mit Hilfe der kristallographischen Gruppentheorie
U. Müller (1997)
10.1103/PhysRevLett.79.4297
OPTIMIZATION BY THERMAL CYCLING
A. Mobius (1997)
10.1021/J100589A006
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
F. Momany (1975)
10.1038/382604A0
De novo design of structure-directing agents for the synthesis of microporous solids
D. Lewis (1996)
GROMOS, Groningen Molecular Simulations, Groningen
W. F. van Gunsteren (1987)
10.1073/PNAS.95.4.1562
Molecular picture of folding of a small α/β protein
F. Sheinerman (1998)
10.1006/JMBI.1996.0139
An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.
F. Fraternali (1996)
10.1073/PNAS.97.19.10383
Native protein sequences are close to optimal for their structures.
B. Kuhlman (2000)
10.1002/(SICI)1521-3773(19990903)38:17<2494::AID-ANIE2494>3.0.CO;2-#
Combinatorial Materials Science and Catalysis.
Jandeleit (1999)
10.1016/S1359-0286(98)80054-5
Ab initio prediction of molecular crystal structures
R. Gdanitz (1998)
10.1063/1.373364
Magnetic diffuse scattering in disordered systems studied by neutron polarization analysis (invited)
J. Stewart (2000)
10.1002/(SICI)1096-987X(199906)20:8%3C786::AID-JCC5%3E3.0.CO;2-B
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
K. Feenstra (1999)
10.1016/S0167-2789(97)00090-0
Multi-basin dynamics of a protein in a crystal environment
A. E. García (1997)
10.1021/JP9728215
Tertiary Structure Prediction of C-Peptide of Ribonuclease A by Multicanonical Algorithm
U. H. Hansmann (1998)
10.1088/0305-4470/31/40/011
Properties of the energy landscape of network models for covalent glasses
J. C. Schön (1998)
10.1021/CM960218D
Crystal Structure Determination from Powder Diffraction Data
K. D. Harris (1996)
10.1016/S0167-2789(97)00106-1
Interaction potentials and inherent structures in liquids, glasses, and crystals
F. Stillinger (1997)
10.1007/BF01016429
Possible generalization of Boltzmann-Gibbs statistics
C. Tsallis (1988)
10.1107/S0108768191014726
The perils of Cc : comparing the frequencies of falsely assigned space groups with their general population
W. Baur (1992)
10.1006/JMBI.1999.2685
Discrimination of the native from misfolded protein models with an energy function including implicit solvation.
T. Lazaridis (1999)
10.1002/(SICI)1096-987X(19980715)19:9<1087::AID-JCC9>3.0.CO;2-M
Searching for saddle points of potential energy surfaces by following a reduced gradient
W. Quapp (1998)
10.1007/PL00006356
On Error Minimization in a Sequential Origin of the Standard Genetic Code
David H. Ardell (1998)
10.1038/31189
Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid
S. Sastry (1998)
10.1063/1.467721
Locating transition states by quadratic image gradient descent on potential energy surfaces
J. Sun (1994)
10.1073/PNAS.96.26.14848
Pressure-induced protein-folding/unfolding kinetics.
N. Hillson (1999)
10.1006/JMBI.1999.2936
Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.
Y. Zhou (1999)
10.1002/CHIN.199826366
Protein Folding: A Perspective from Theory and Experiment
C. Dobson (1998)
10.1038/29487
Archetypal energy landscapes
D. Wales (1998)
10.1002/(SICI)1097-0134(19991115)37:3<485::AID-PROT15>3.0.CO;2-G
Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins
S. S. Brody (1999)
10.1524/ZKRI.1997.212.8.553
The 3-regular nets with four and six vertices per unit cell
M. Bader (1997)
10.1016/S0167-2738(00)00632-9
Zeolites and catalysis
J. Weitkamp (2000)
10.1126/science.220.4598.671
Optimization by Simulated Annealing
S. Kirkpatrick (1983)
Statistical Physcis, Part 1, 3rd Ed., Pergamon
L. D. Landau (1980)
10.1103/PHYSREVA.51.R1
Zero-kinetic-energy electron spectroscopy of the predissociating A2 Sigma + state of HBr+
Mank (1995)
10.1021/AR960288Q
Theory of Two-State Cooperative Folding of Proteins
M. Hao (1998)



This paper is referenced by
10.1039/B709943F
Global exploration of the energy landscape of solids on the ab initio level.
K. Doll (2007)
10.1002/asia.201200794
Structure prediction of binary pernitride MN2 compounds (M=Ca, Sr, Ba, La, and Ti).
A. Kulkarni (2013)
10.1002/ZAAC.200400542
Prediction of Possible High-Pressure Phases of Cu3N†
Z. Cancarevic (2005)
10.1002/ANGE.200504510
“Design” in der chemischen Synthese – eine Fiktion?†
M. Jansen (2006)
10.1039/B506031A
Rational design of new inorganic compounds with the ZrSiCuAs structure type using 2D building blocks
H. Kabbour (2005)
Point-Pattern Matching Technique for Local Structural Analysis in Condensed Matter
Arash Dehghan Banadaki (2018)
10.1154/1.1483322
Modeling of hP3 intermetallics in space group P-3m1: Calculated powder patterns from CRYSTMET ® X-ray cell data and ab initio coordinates
Y. L. Page (2002)
10.1063/1.2711431
Ab initio prediction of the low-temperature phase diagrams in the systems KBr-NaBr, KX-RbX, and LiX-RbX (X=Cl,Br).
I. Pentin (2007)
10.1016/S0009-2614(01)01452-X
Gaining insights into the evolutionary behaviour in genetic algorithm calculations, with applications in structure solution from powder diffraction data
S. Habershon (2002)
10.1002/ANGE.201109030
Vom Konzept lokaler Ergodizität hin zu erweiterten Phasendiagrammen
S. Woodley (2012)
10.1002/asia.200700323
Stability of alkali metal halide polymorphs as a function of pressure.
Ž. Čančarević (2008)
10.1063/1.4765700
Experimental and theoretical study on Raman spectra of magnesium fluoride clusters and solids.
S. Neelamraju (2012)
10.1002/ANIE.200462170
The metal flux: a preparative tool for the exploration of intermetallic compounds.
M. Kanatzidis (2005)
10.1039/C3RA41477A
Determination of the energy landscape of Pd12Pt1 using a combined genetic algorithm and threshold energy method
Rafael Pacheco-Contreras (2013)
10.4028/www.scientific.net/MSF.453-454.71
Structure Prediction of Solids: Heuristic Algorithms for Local Optimization on Hartree-Fock Level
Ž. Čančarević (2004)
10.1002/anie.201008070
Ab initio energy landscape of GeF2 : a system featuring lone pair structure candidates.
K. Doll (2011)
10.1088/1367-2630/9/2/026
Cu-based metalorganic systems: an ab initio study of the electronic structure
L. Salguero (2006)
10.1002/anie.200802365
Opening the "stable" door.
M. Rosseinsky (2008)
10.1002/ZAAC.200400338
Structure Prediction of Inorganic Nanoparticles with Predefined Architecture using a Genetic Algorithm
S. Woodley (2004)
10.1524/zkri.2007.222.3-4.105
Direct space methods of structure determination from powder diffraction: principles, guidelines and perspectives
R. Černý (2007)
10.1039/B312526B
The prediction of inorganic crystal framework structures using excluded regions within a genetic algorithm approach.
S. Woodley (2004)
10.1039/c004040c
Ab initio prediction of low-temperature phase diagrams in the Al-Ga-In-As system, MAs-M'As (M, M' = Al, Ga or In) and AlAs-GaAs-InAs, via the global study of energy landscapes.
I. Pentin (2010)
10.1038/s41598-020-64030-3
Ab Initio Prediction of the Phase Transition for Solid Ammonia at High Pressures
L. Huang (2020)
10.1021/acs.jctc.6b00118
A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide.
S. Neelamraju (2016)
10.1039/B517447C
Ab initio computation of low-temperature phase diagrams exhibiting miscibility gaps.
J. C. Schön (2006)
10.1002/PSSB.200945246
Predicting solid compounds via global exploration of the energy landscape of solids on the ab initio level without recourse to experimental information
J. C. Schön (2010)
10.1039/c8fd00060c
What is the best or most relevant global minimum for nanoclusters? Predicting, comparing and recycling cluster structures with WASP@N.
S. Woodley (2018)
The State Space of Complex Systems
Dipl.-Phys. Frank Heilmann (2005)
10.1039/B315216M
Prediction of inorganic crystal framework structures
S. Woodley (2004)
10.1016/B978-0-08-102232-0.09991-7
Introduction to modeling nanoclusters and nanoparticles
S. Woodley (2018)
10.1002/ANGE.200462170
Metallische Schmelzen – Reaktionsmedien zur Präparation intermetallischer Verbindungen
M. Kanatzidis (2005)
10.1007/978-3-319-50257-1_75-1
Stochastic Surface Walking Method and Applications to Real Materials
C. Shang (2019)
See more
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