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Global Optimization Approaches in Protein Folding and Peptide Docking (1999)  (Make Corrections)  (2 citations)
C.A. Floudas, J.L. Klepeis, P.M. Pardalos
Proceedings of DYCOPS-5 on Dynamics and Control of Process Systems



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Abstract: . The recent advances in genetic engineering, high powered computing and global optimization continue to stimulate interest in the area of molecular modeling and protein structure prediction. The goal of these efforts is the ability to correctly predict native protein conformations and the binding interactions of macromolecules. These two problems currently dominate the field of computational chemistry and, through the use of detailed molecular models, they have also greatly influenced research ... (Update)

Context of citations to this paper:   More

...spatial branch and bound approach for the global optimization of MINLP problems. Klepeis et al. 1998) and Klepeis and Floudas (1998) proposed new global optimization approaches for the structure prediction of solvated peptides using the area and the volume...

...to the global minimum energy structure. A number of recent reviews have focused on global optimization issues for these systems [13, 28, 30, 33]. In this work, the global optimization approach ffBB has been extended to identifying global minimum energy conformations of...

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Protein Folding and Peptide Docking: A Molecular.. - Klepeis.. (1998)   (Correct)
Recent Advances in Global Optimization for Process Synthesis.. - Floudas (1999)   (Correct)

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4:   Global minimum potential energy conformations of oligopeptides (context) - Androulakis, Maranas et al.
2:   for General Twice--Differentiable NLPs (context) - Adjiman, Dallwig et al.
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BibTeX entry:   (Update)

C. A. Floudas, J.L. Klepeis, and P.M. Pardalos. Global Optimization Approaches In Protein Folding and Peptide Docking. In F. Roberts (Ed.), editor, DIMACS Series In Discrete Mathematics and Theoretical Computer Science, 1998. in press. http://citeseer.ist.psu.edu/floudas99global.html   More

@inproceedings{ floudas98global,
    author = "C. A. Floudas",
    title = "Global Optimization Approaches in Protein Folding and Peptide Docking",
    booktitle = "Proceedings of {DYCOPS}-5 on Dynamics and Control of Process Systems",
    pages = "167--178",
    year = "1998",
    url = "citeseer.ist.psu.edu/floudas99global.html" }
Citations (may not include all citations):
1527   Optimization by simulated annealing - Kirkpatrick, Jr et al. - 1983  ACM
1051   optimization and machine learning (context) - Goldberg, in - 1989
643   Equation of state calculations by fast computing machines (context) - Metropolis, Rosenbluth et al. - 1953
71   Handbook of Global Optimization (context) - Horst, Pardalos - 1995
35   Solvent accessible surfaces of proteins and nucleic acids (context) - Connolly - 1983
34   Analytical molecular surface calculation (context) - Connolly - 1983
32   Calculation of conformational ensembles from potentials of m.. (context) - Sippl - 1990
28   A geometric approach to macromolecule-ligand interactions (context) - Kuntz, Blaney et al. - 1982
27   The interpretation of protein structures : estimation of sta.. (context) - Lee, Richards - 1971
25   Global minimum potential energy conformations of small molec.. (context) - Maranas, Floudas - 1994
25   Global minimum potential energy conformations of oligopeptid.. (context) - Androulakis, Maranas et al. - 1997
24   Genetic algorithms and the optimal allocation of trials (context) - Holland - 1973  DBLP
23   The multiple-minima problem in the conformational analysis o.. (context) - Piela, Kostrowicki et al. - 1989
23   the multiple-minima problem in conformational analysis of po.. (context) - Piela, Scheraga - 1987
22   Reduced representation model of protein structure prediction.. (context) - Sun - 1993
21   CHARMM : A program for macromolecular energy minimization an.. (context) - Brooks, Bruccoleri et al. - 1983
21   ffBB: A global optimization method for general constrained n.. - Androulakis, Maranas et al. - 1995
19   Rigorous convex underestimators for general twicedifferentia.. - Adjiman, Floudas - 1996
19   Genetic algorithms : Principles of natural selection applied.. (context) - Forrest - 1993
19   Do intelligent configuration search techniques outperform ra.. (context) - Judson, Colvin et al. - 1992
19   A new force field for molecular mechanical simulation of nuc.. (context) - Weiner, Kollman et al. - 1984
18   Molecular modeling of proteins and mathematical prediction o.. - Neumaier - 1997  ACM
18   Packet annealing : A deterministic method for global minimiz.. (context) - Shalloway - 1992
16   A global optimization approach for Lennard-Jones microcluste.. - Maranas, Floudas - 1992
16   The kinetics of formation of native ribonuclease during oxid.. (context) - Anfinsen, Haber et al. - 1961
16   Application of the renormalization group to deterministic gl.. (context) - Shalloway - 1992
15   An all atom force field for simulations of proteins and nucl.. (context) - Weiner, Kollman et al. - 1986
14   A parallel build-up algorithm for global energy minimization.. - Coleman, Shalloway et al. - 1994
13   Application of the diffusion equation method for global opti.. (context) - Kostrowicki, Scheraga - 1992
13   Automated docking of substrates to proteins by simulated ann.. (context) - Goodsell, Olson - 1990
13   Monte Carlo minimization approach to the multiple-minima pro.. (context) - Li, Scheraga - 1987
13   Nonlinear and Mixed-Integer Optimization : Fundamentals and .. (context) - Floudas - 1995
13   Protein folding by restrained energy minimization and molecu.. - Levitt - 1983
11   Solvation energy in protein folding and binding (context) - Eisenberg, McLachlan - 1986
11   A survey of methods for searching the conformational space o.. (context) - Leach - 1991
11   for general twice-differentiable NLPs (context) - Adjiman, Dallwig et al. - 1998
11   for general twice-differentiable NLPs - II (context) - Adjiman, Androulakis et al. - 1998
11   Optimization methods for computing global minima of nonconve.. (context) - Pardalos, Shalloway et al. - 1994
11   Molecular structure determination by convex global underesti.. - Phillips, Rosen et al. - 1996
10   Molecular dynamics on deformed potential energy hypersurface.. (context) - Pillardy, Piela - 1995
10   A new approach to the rapid determination of protein side ch.. (context) - Tuffery, Etchebest et al. - 1991
10   Global optimization for molecular conformation problems (context) - Maranas, Floudas - 1993
10   Global minimization of nonconvex energy functions : Molecula.. (context) - Pardalos, Shalloway et al. - 1996
10   Predicting three-dimensional structures of oligopeptides (context) - Scheraga - 1992
10   Electrostatics in biomolecular structure and dynamics (context) - Davis, McCammon - 1990
9   Flexible ligand docking using a genetic algorithm (context) - Oshiro, Kuntz et al. - 1995  DBLP
9   The application of the genetic algorithm to the minimization.. (context) - Le Grand, Merz - 1993
9   An approach to the multiple-minima problem in protein foldin.. (context) - Purisima, Scheraga - 1987
9   Global optimization of MINLP problems (context) - Adjiman, Androulakis et al. - 1997
9   Protein folding funnels : A kinetic approach to the sequence.. (context) - Leopold, Montal et al. - 1992
8   A deterministic global optimization approach for molecular s.. (context) - Maranas, Floudas - 1994
8   A global optimization method (context) - Adjiman, Androulakis et al. - 1996
8   Soft docking (context) - Jiang, Kim - 1991
8   Atomic solvation parameters applied to molecular dynamics of.. (context) - Wesson, Eisenberg - 1992
8   Protein docking and complementarity (context) - Shoichet, Kuntz - 1991
7   ffl-optimal solutions to distance geometry problems via glob.. (context) - Mor'e, Wu - 1996
7   Free energies of hydration of solute molecules (context) - Kang, Gibson et al. - 1988
7   A computational procedure for determining energetically favo.. (context) - Goodford - 1985
7   Conformational analysis of flexible ligands in macromolecula.. (context) - Leach, Kuntz - 1992  ACM
7   State of the Art in Global Optimization : Computational Meth.. (context) - Floudas, Pardalos - 1996
7   Free energies of hydration of solute molecules (context) - Kang, N'emethy et al. - 1987
7   Computational alchemy (context) - Straatsma, McCammon - 1992
7   A deterministic global optimization approach for the protein.. - Maranas, Androulakis et al. - 1996
7   Free energies of hydration of solute molecules (context) - Kang, N'emethy et al. - 1987
7   Realistic simulations of native-protein dynamics in solution.. (context) - Daggett, Levitt - 1993
7   Free energies of hydration of solute molecules (context) - Kang, N'emethy et al. - 1987
6   Docking by least-squares fitting of molecular surface patter.. (context) - Bacon, Moult - 1992
6   Multicanonical ensemble - a new approach to simulate 1 st or.. (context) - Berg, Neuhaus - 1992
6   Deterministic global optimization in design (context) - Floudas - 1997
6   Shape complementarity at the hemoglobin ff 1 fi 1 subunit in.. (context) - Connolly - 1986
6   Numerical comparisons of three recently proposed algorithms .. (context) - Hansmann, Okamoto - 1997  DBLP
6   A multiple-start Monte Carlo docking method (context) - Hart, Read - 1992
6   Molecular recognition of receptor sites using a genetic algo.. (context) - Jones, Willett et al. - 1995
6   CGU : An algorithm for molecular structure prediction - Dill, Phillips et al. - 1997
6   Intermediates in the folding reactions of small proteins (context) - Kim, Baldwin - 1990
6   Monte Carlo docking of oligopeptides to proteins (context) - Calfisch, Niederer et al. - 1992
5   Automated docking with grid-based energy evaluation (context) - Meng, Shoichet et al. - 1992  ACM
5   Conformational energy calculations on polypeptides and prote.. (context) - V'asquez, N'emethy et al. - 1994
5   Free energy calculations : Applications to chemical and bioc.. (context) - Kollman - 1993
5   Crystal structure of the human class II MHC protein HLA-DR1 .. (context) - Stern, Brown et al. - 1994
5   and intrinsic torsional potentials for the naturally occurri.. (context) - Momany, McGuire et al. - 1975
5   Accessible surface areas as a measure of the thermodynamic p.. (context) - Ooi, Oobatake et al. - 1987
5   Energy minimizations for crystals of cyclic peptides and cra.. (context) - Jorgensen, Tirado-Rives et al. - 1988
5   Empirical solvation models can be used to differentiate nati.. (context) - Vila, Williams et al. - 1991
5   Biased probability Monte Carlo conformational searches and e.. (context) - Abagyan, Totrov - 1994
5   Calculating the electrostatic potential of molecules in solu.. (context) - Gilson, Sharp et al. - 1988
5   Improved geometrical parameters and nonbonded interactions f.. (context) - N'emethy, Gibson et al. - 1992
5   Groningen Molecular Simulation (context) - van Gunsteren, Berendsen - 1987
4   A comparative study of global minimum energy conformations o.. - Klepeis, Floudas
4   Protein-protein recognition analyzed by docking simulation (context) - Cherfils, Duquerroy et al. - 1991
4   Intermolecular potentials from crystal data (context) - Momany, Carruthers et al. - 1974
4   Nonlinear optimization simplified by hypersurface deformatio.. (context) - Stillinger, Weber - 1988
4   Empirical solvation models in the context of conformational .. (context) - Williams, Vila et al. - 1992
4   Optimization methods in computational chemistry (context) - Schlick - 1992
4   differentiable hydration potential for peptides and proteins (context) - Augspurger, Scheraga et al. - 1996
4   Improved strategy in analytic surface calculation for molecu.. (context) - Eisenhaber, Argos - 1993
4   Predicting solvated peptide conformations via global minimiz.. - Klepeis, Androulakis et al. - 1998
4   Determining minimum energy conformations of polypeptides by .. (context) - Vajda, De Lisi - 1990
4   and hydrogen bond interactions for the naturally occurring a.. (context) - N'emethy, Pottle et al. - 1983
4   Peptide docking using dynamic programming (context) - Gulukota, Vajda et al. - 1996  DBLP
4   Intermolecular potentials from crystal data (context) - Momany, Carruthers et al. - 1974
3   Simulations of peptide conformational dynamics and thermodyn.. (context) - Case - 1993
3   CLIX: A search algorithm for finding novel ligands capable o.. (context) - Lawrence, Davis - 1992
3   Are there pathways to protein folding (context) - Levinthal - 1968
3   the multiple-minima problem in the conformational analysis o.. (context) - Ripoll, Scheraga - 1990
3   The multiple minima problem in the conformational analysis o.. (context) - Ripoll, Scheraga - 1989
3   Crystal structures of two viral peptides in complex with mur.. (context) - Fremont, Matsumura et al. - 1992
3   Thermodynamics and kinetics of protein folding (context) - Sali, Shaknovich et al. - 1996
3   A hydrocarbon force field utilizing V 1 and V2 torsional ter.. (context) - Allinger, analysis - 1977
3   The MM3 force field for hydrocarbons (context) - Allinger, Yuh et al. - 1989
3   Tracking metastable states to free-energy global minima (context) - Church, Oresic et al. - 1996
3   Analysis of the contribution of internal vibrations to the s.. (context) - Scheraga - 1969
3   Computational methods to predict binding free energy in liga.. (context) - Jain, Murcko - 1995
3   Empirical potentials and functions for protein folding and b.. (context) - Vajda, Sippl et al. - 1997
3   Use of buildup and energy-minimization procedures to compute.. (context) - Vasquez, Scheraga - 1985
3   Determination of threedimensional structure of proteins by s.. (context) - Nilges, Gronenborn et al. - 1988
3   Docking flexible molecules: a case study of three proteins (context) - Judson, Tan et al. - 1995  DBLP
3   A prediction of tertiary structures of peptide by the Monte .. (context) - Kawai, Kikuchi et al. - 1989
3   Electrostatic energy and macromolecular function (context) - Warshel, Aqvist - 1991
3   Conformational analysis of flexible molecules : Location of .. (context) - Wilson, Cui et al. - 1988
3   Computer analysis of protein-protein interactions (context) - Wodak, Janin - 1978
3   Some approaches to the multiple-minima problem in protein fo.. (context) - Kostrowicki, Scheraga - 1996
3   A predictive method for the evaluation of peptide binding in.. - Androulakis, Nayak et al. - 1997
2   Using shape complementarity as an initial screen in designin.. (context) - DesJarlais, Sheridan et al. - 1988
2   Efficiency of Monte Carlo minimization procedures and their .. (context) - Meirovitch, Meirovitch - 1997  DBLP
2   Structure and free energy of complex thermodynamic systems (context) - Li, Scheraga - 1988
2   Prediction of peptide conformation by multicanonical algorit.. (context) - Hansmann, Okamoto - 1993
2   Crown ether-neutral molecule interactions studied by molecul.. (context) - Grootenhuis, Kollman - 1989
2   quasi-flexible (context) - Miller, Kearsley et al. - 1994
2   Functionality maps of binding sites: a multicopy simultaneou.. (context) - Miranker, Karplus - 1991
2   What determines the strength of noncovalent association of l.. (context) - Miyamoto, Kollman - 1993
2   Application to antigen recognition by class I major histocom.. (context) - Rosenfeld, Zheng et al. - 1993
2   The multiple-minima problem in small peptides revisited (context) - Morales, no-Ju'arez et al. - 1992
2   Ludi: Rule-based automatic design of new substituents for en.. (context) - Bohm - 1992  DBLP
2   Foundations of rotational isomeric state theory and general .. (context) - Flory - 1974
2   An approach to the multiple-minima problem by relaxing dimen.. (context) - Purisima, Scheraga - 1986
2   The double cubic lattice method : Efficient approaches to nu.. (context) - Eisenhaber, Lijnzaad et al. - 1995
2   Computer studies of interactions between macromolecules (context) - Wodak, De Crombrugghe et al. - 1987
2   A comparative study of the simulated annealing and Monte Car.. (context) - Nayeem, Vila et al. - 1991
2   Necessary conditions for avoiding incorrect polypeptide fold.. (context) - Vajda, Jafri et al. - 1993
2   Multiple copy simultaneous search and construction of ligand.. (context) - Calfisch, Miranker et al. - 1993
2   Normal mode analysis of protein dynamics (context) - Case - 1994
2   Flexibases: a way to enhance the use of molecular docking me.. (context) - Kearsley, Underwood et al. - 1994
2   VALIDATE : a new method for receptor-based prediction of bin.. (context) - Head, Smyte et al. - 1996
2   Prediction of low-energy structures of metenkephalin by Mont.. (context) - Okamoto, Kikuchi et al. - 1992
2   Free energy calculations for peptides using a deterministic .. (context) - Klepeis, Floudas
2   Protein conformation of a lattice model using tabu search (context) - Pardalos, Liu et al. - 1997  ACM
2   Why energy embedding works (context) - Crippen - 1987
2   Global energy minimization by rotational energy embedding (context) - Crippen, Havel - 1990  ACM   DBLP
2   Structure and energetics of ligand-binding to proteins - Esc.. (context) - Dauber-Osguthorpe, Roberts et al. - 1988
2   New theoretical methodology for elucidating the solution str.. (context) - Meirovitch, Meirovitch - 1996
1   Free energy calculations in molecular biophysics (context) - Reynolds, King et al. - 1992
1   Automatic identification of topographic surface features (context) - Lee, Rose et al. - 1985
1   The genetic algorithm and protein tertiary structure predict.. (context) - Le Grand, Merz - 1994
1   Thermodynamic Theory of Site-Specific Binding Processes in B.. (context) - Di Cera - 1995
1   Computer design of bioactive molecules: a method for recepto.. (context) - Moon, Howe - 1991
1   A combined iterative and boundary element approach for solut.. (context) - Vorobjev, Grant et al. - 1992
1   Applications of simulated annealing to the multiple-minima p.. (context) - Morales, no-Ju'arez et al. - 1991
1   Grid-search molecular accessible surface algorithm for solvi.. (context) - Wang - 1991  ACM
1   of bovine pancreatic trypsin inhibitor as predicted by Monte.. (context) - Nakazawa, Kawai et al. - 1992
1   Comparative study of multicanonical and simulated annealing .. - Hansmann, Okamoto - 1994
1   Vibrational frequencies and thermodynamics (context) - Lii, Allinger et al. - 1989
1   A free energy based Monte Carlo minimization procedure for b.. (context) - V'asquez, Meirovitch et al. - 1994
1   the use of classical statistical mechanics in the treatment .. (context) - Scheraga - 1976
1   Crystallographic refinement by simulated annealing (context) - Brunger - 1988  ACM
1   Refinement of the influenza virus hemagglutinin by simulated.. (context) - Weis, Brunger et al. - 1990
1   Calculation of binding energy differences for receptor-ligan.. (context) - Shen, Quiocho - 1995
1   Minimization of empirical energy functions in proteins inclu.. (context) - von Freyberg, Braun - 1993  ACM
1   Reaction pathway for the quartenary structure change in hemo.. (context) - Janin, Wodak - 1985
1   Polymer-solvent interactions for homopolypeptides in aqueous.. (context) - Hopfinger - 1971
1   The van der Waals' potentials and crystal data for aliphatic.. (context) - Lii, Allinger et al. - 1989
1   Method for estimating the configurational entropy of macromo.. (context) - Karplus, Kushick - 1981
1   Eskow and R (context) - Shao, Byrd
1   GensStar: a program for de novo drug design (context) - Rotstein, Murcko - 1993
1   Calculation of hydration free energy for a solute with many .. (context) - Kinoshita, Okamoto et al. - 1997  DBLP
1   GroupBuild: a fragment-based method for de novo drug design (context) - Rotstein, Murcko - 1993
1   ff-helix folding by Monte Carlo simulated annealing in isola.. (context) - Okamoto, Fukugita et al. - 1991
1   Multiple-start Monte Carlo docking of flexible ligands (context) - Hart, Read - 1994
1   Landes Company and Chapman & Hall (context) - Urban, Chicz et al. - 1996
1   Powerful simulated annealing algorithm locates global minima.. (context) - Snow - 1992
1   Multicanonical algorithms for 1st order phase-transitions (context) - Berg, Neuhaus - 1991
1   Revised algorithms for the build-up procedure for predicting.. (context) - Gibson, Scheraga - 1987
1   Maigret and H (context) - Perrot, Cheng et al. - 1992
1   An empirical hydrogen bond potential function based on molec.. (context) - McGuire, Momany et al. - 1972
1   The computer program Ludi: A new method for the de novo desi.. (context) - Bohm - 1992
1   Determination of an empirical energy function for protein co.. (context) - Crippen, Ponnuswamy - 1987
1   Efficient search for all low energy conformations of polypep.. (context) - von Freyberg, Braun - 1991
1   Atomic structure of a human MHC molecule presenting an influ.. (context) - Silver, Guo et al. - 1992
1   Empirical free energy calculations of ligand-protein crystal.. (context) - Verkhivker, Appelt et al. - 1995
1   The electrostatically driven Monte Carlo method - Applicatio.. (context) - Ripoll, V'asquez et al. - 1991
1   Structure Based Design of Nonpeptide Inhibitors Specific for.. (context) - DesJarlais, Seibel et al. - 1990

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