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7
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0027859028
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Molecular modeling methods: basic techniques and challenging problems
-
of special interest, This paper provides a succint overview of a number of computational techniques based on potential energy functions that are used routinely in rational drug-design applications.
-
(1993)
Pharmacol Ther
, vol.60
, pp. 149-167
-
-
Lesyng1
McCammon2
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10
-
-
0027486356
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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. 2. CO and dioxygen binding to myoglobin
-
(1993)
Protein Sci
, vol.2
, pp. 1975-1986
-
-
Lopez1
Kollman2
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11
-
-
0028230038
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Structure and dynamics of the active site gorge of acetylcholinesterase — synergistic use to molecular dynamics simulation and X-ray crystallography
-
(1994)
Protein Sci
, vol.3
, pp. 188-197
-
-
Axelsen1
Harel2
Silman3
Sussman4
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12
-
-
0027280497
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Computer modelling studies on the binding of 2′, 5′-linked dinucleoside phosphates to ribonuclease T1 — influence of subsite interactions on the substrate specificity
-
(1993)
J Biomol Struct Dyn
, vol.10
, pp. 891-904
-
-
Balaji1
Saenger2
Rao3
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13
-
-
0028362040
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Molecular dynamics study of the binding of phenylalanine stereoisomers of thermolysin
-
(1994)
Biophys Chem
, vol.50
, pp. 237-248
-
-
Ghosh1
Edholm2
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14
-
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0028179616
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“Open back door’ in a molecular dynamics simulation of acetylcholinesterase
-
of special interest, This paper illustrates nicely the power of computational methods in the study of ligand—protein complexes. Using Poisson—Boltzmann electrostatics calculations and molecular dynamics simulations, and authors propose the presence of an alternative entrance to the active site of acetylcholinesterase, and suggest a mutation to test this hypothesis. Resuts from enzyme kinetics studies of acetylcholinesterase are better understood in the context of this alternative active-site entrance, and it is unlikely than an alternative active-site entrance would have been considered without the molecular modeling results
-
(1994)
Science
, vol.263
, pp. 1276-1278
-
-
Gilson1
Straatsma2
McCammon3
Ripoll4
Faerman5
Axelson6
Silman7
Sussman8
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16
-
-
0027139338
-
Affinity and specificity of serine endopeptidase protein inhibitor interactions — empirical free energy calculations based on X-ray crystallographic structures
-
(1993)
J Mol Biol
, vol.234
, pp. 661-679
-
-
Krystek1
Stouch2
Novotny3
-
18
-
-
0028339543
-
Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking: application to an operator mutation in the λ repressor-operator complex
-
of special interest, These authors report on the use of systematic conformational search and Poisson—Boltzmann electrostatics calculations to compute energies of complex formation for the lambda repressor with its DNA operator sequence. This is one of the first examples of the application of this technique to estimate energies of complex formation.
-
(1994)
J Mol Biol
, vol.238
, pp. 455-465
-
-
Zacharias1
Luty2
Davis3
McCammon4
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19
-
-
0000967631
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A comparison of perturbation methods and Poisson-Boltzmann electrostatics calculations for estimation of relative solvation free energies
-
(1994)
J Phys Chem
, vol.98
, pp. 1748-1752
-
-
Ewing1
Lybrand2
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20
-
-
0001650642
-
A good ligand is hard to find: automated docking methods
-
of special interest, This manuscript is an excellent recent review of ligand-docking techniques now in common use. Different algorithms are described, and the strengths and limitations of docking methods are discussed.
-
(1993)
Perspect Drug Discov Des
, vol.1
, pp. 301-319
-
-
Blaney1
Dixon2
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21
-
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0027480452
-
Structure-based inhibitor design by using protein models for the development of antiparasitic agents
-
of outstanding interest, Standard ligand-docking methods were used to probe the Fine Chemicals Directory database for candidate inhibitors of cercarial elastase from schistosomes and cysteine protease from malarial trophozoite. An inhibitor of modest affinity was identified for each enzyme, serving as a suitable lead compound for further development in each case. This paper nicely illustrates the power of homology model building (for construction of the receptor-site models) and ligand docking, coupled with classic enzymology, to discover novel enzyme inhibitors with therapeutic potential.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 3583-3587
-
-
Ring1
Sun2
McKerrow3
Lee4
Rosenthal5
Kuntz6
Cohen7
-
25
-
-
0028412035
-
FLOG: a system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure
-
of special interest, This paper describes the use of databases containing multiple conformations of a particular ligand as a simple strategy to address ligand flexibility in standard docking algorithms.
-
(1994)
J Comput Aided Mol Des
, vol.8
, pp. 153-174
-
-
Miller1
Kearsley2
Underwood3
Sheridan4
-
28
-
-
0027135804
-
Computing the structure of bound peptides — application to antigen recognition by class-I major histocompatibility complex receptors
-
of special interest, Multiple copy simultaneous search techniques are used to identify the optimal binding mode for peptide ligand in a class I major histocompatibility complex receptor. In this study, the receptor is fixed in a conformation that was observed crystallographically, and multiple peptide fragments were docked simultaneously
-
(1993)
J Mol Biol
, vol.234
, pp. 515-521
-
-
Rosenfeld1
Zheng2
Vajda3
DeLisi4
-
30
-
-
0028158936
-
Ligand docking to proteins with discrete side chain flexibility
-
of special interest, This work incorporates both ligand flexibility (via a systematic conformational search) and limited receptor flexibility via sampling of allowable side-chain conformations of amino acids in the binding pocket. This strategy affords a reasonably efficient mechanism to include modest flexibility in a traditional ligand-protein docking study
-
(1994)
J Mol Biol
, vol.235
, pp. 345-356
-
-
Leach1
-
31
-
-
0027327164
-
Syntheses of pseudo-.ALPHA.-D-glucopyranose, pseudo-.BETA.-D-glucopyranose, and validamine from D-glucuronolactone.
-
of special interest, See annotation [32].
-
(1993)
CHEMICAL & PHARMACEUTICAL BULLETIN
, vol.41
, pp. 1197-1202
-
-
Yamada1
Itai2
-
32
-
-
0027169710
-
Application and evaluation of the automated docking method
-
of special interest, This paper and [31] describe an alternative approach to account for ligand and receptor flexibility in a docking search. This method uses a systematic conformational search for the ligand, then prescreens docked ligand—receptor complexes for those with optimal hydrogen-bonded contacts before energy minimization of the complex is performed to allow for flexibility of the receptor site.
-
(1993)
Chem Pharm Bull (Tokyo)
, vol.41
, pp. 1203-1206
-
-
Yamada1
Itai2
-
35
-
-
0028282687
-
HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecular binding site
-
(1994)
Proteins
, vol.19
, pp. 199-221
-
-
Eisen1
Wiley2
Karplus3
Hubbard4
-
37
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
of special interest, A description of an empirical continuum method for calculation of solvation energies of small molecules. Poisson—Boltzmann calculations are used to handle electrostatic effects, and a surface area term, calibrated against experimental data to reproduce hydrocarbon solvation energies, is used to handle non-polar effects. Very good agreement with experimental solvation energies is obtained for a wide range of small organic molecules.
-
(1994)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff1
Sharp2
Honig3
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