Computational tools for structure-based ligand design (Q41585193)

4 October 2017

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title

Computational tools for structure-based ligand design (English)

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4 October 2017

Böhm HJ

1

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4 October 2017

1 January 1996

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Progress in Biophysics and Molecular Biology

4 October 2017

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4 October 2017

66

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4 October 2017

3

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4 October 2017

197-210

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The development of versions 3 and 4 of the Cambridge Structural Database System

4 October 2017

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Computational methods to predict binding free energy in ligand-receptor complexes

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The art and practice of structure-based drug design: A molecular modeling perspective

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The computer program LUDI: a new method for the de novo design of enzyme inhibitors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Towards the automatic design of synthetically accessible protein ligands: peptides, amides and peptidomimetics

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Current computational tools for de novo ligand design

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Molecular modeling software and methods for medicinal chemistry

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Shape distributions of protein topography

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

General parameterized SCF model for free energies of solvation in aqueous solution

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Nonpeptidic inhibitors of human neutrophil elastase. 7. Design, synthesis, and in vitro activity of a series of pyridopyrimidine trifluoromethyl ketones

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

De novo design of enzyme inhibitors by Monte Carlo ligand generation

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Application of the three-dimensional structures of protein target molecules in structure-based drug design

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Molecular docking towards drug discovery

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Design and synthesis of potent and highly selective thrombin inhibitors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Classical electrostatics in biology and chemistry

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Calculation of the free energy of association for protein complexes

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Structure-based strategies for drug design and discovery

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Ligand docking to proteins with discrete side-chain flexibility.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Determination of clefts in receptor structures.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Current methods for site-directed structure generation.

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Design, synthesis and biological activity of novel rigid amidino-phenylalanine derivatives as inhibitors of thrombin

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

3D database searching in drug design

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

SPROUT: 3D Structure Generation Using Templates

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Bis tertiary amide inhibitors of the HIV-1 protease generated via protein structure-based iterative design.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Automated docking with grid-based energy evaluation

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Orientational sampling and rigid-body minimization in molecular docking

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Functionality maps of binding sites: a multiple copy simultaneous search method

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Computer design of bioactive molecules: a method for receptor-based de novo ligand design

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Flexible ligand docking using a genetic algorithm.

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

CONCERTS: dynamic connection of fragments as an approach to de novo ligand design

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Rational modification of human synovial fluid phospholipase A2 inhibitors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Placement of medium-sized molecular fragments into active sites of proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

GroupBuild: a fragment-based method for de novo drug design

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Automatic generation of 3D-atomic coordinates for organic molecules

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2

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https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Structure-based discovery of inhibitors of thymidylate synthase

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypotheses.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Synthesis and biological evaluation of novel 2,6-diaminobenz[cd]indole inhibitors of thymidylate synthase using the protein structure as a guide

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Structure-based drug design: progress, results and challenges

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Rational design of potent sialidase-based inhibitors of influenza virus replication

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

A possible involvement of solvent-induced interactions in drug design

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

Allosteric modifiers of hemoglobin. 2. Crystallographically determined binding sites and hydrophobic binding/interaction analysis of novel hemoglobin oxygen effectors

1 reference

https://api.crossref.org/works/10.1016%2FS0079-6107%2897%2900005-9

7 January 2021

10.1016/S0079-6107(97)00005-9

Identifiers

DOI

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4 October 2017

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PubMed ID

9284450