Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs (Q28285760)

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English	Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs	scientific article

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Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs (English)

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author name string

H J Böhm

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publication date

July 1998

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Journal of Computer - Aided Molecular Design

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12

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4

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309-23

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[Inhibition of thrombin, plasmin and trypsin effect by alkyl- and alkoxybenzamidine]

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Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol

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Design and synthesis of potent and highly selective thrombin inhibitors

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

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A pre-transition-state mimic of an enzyme: X-ray structure of adenosine deaminase with bound 1-deazaadenosine and zinc-activated water

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Possible transition-state analogs for ribonuclease. Complexes of uridine with oxovanadium(IV) ion and vanadium(V) ion

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Structure-based strategies for drug design and discovery

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Inhibition of bovine and human thrombins by derivatives of benzamidine

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On the rational design of renin inhibitors: X-ray studies of aspartic proteinases complexed with transition-state analogues

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Contribution of buried hydrogen bonds to protein stability. The crystal structures of two barnase mutants

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Thiorphan and retro-thiorphan display equivalent interactions when bound to crystalline thermolysin

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Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate

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Calorimetric study of concanavalin A binding to saccharides.

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Solvent-accessible surfaces of proteins and nucleic acids

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

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Hemagglutinins from two influenza virus variants bind to sialic acid derivatives with millimolar dissociation constants: a 500-MHz proton nuclear magnetic resonance study

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Structural analysis of a series of antiviral agents complexed with human rhinovirus 14.

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

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Automated site-directed drug design using molecular lattices

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

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Analogous inhibitors of elastase do not always bind analogously

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Detection, delineation, measurement and display of cavities in macromolecular structures

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Aromatic-aromatic interaction: a mechanism of protein structure stabilization

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HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

1 reference

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Quantum mechanical model assembly study on the energetics of binding of arabinose, fucose, and galactose to L-arabinose-binding protein.

1 reference

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Selective inhibition of thrombin by (2R,4R)-4-methyl-1-[N2-[(3-methyl-1,2,3,4-tetrahydro-8-quinolinyl++ +) sulfonyl]-l-arginyl)]-2-piperidinecarboxylic acid

1 reference

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Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes

1 reference

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Contribution of hydrogen bonding to the conformational stability of ribonuclease T1

1 reference

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Hydrophobic binding site in acetylcholinesterase

1 reference

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

1 reference

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Flavin-oxygen derivatives involved in hydroxylation by p-hydroxybenzoate hydroxylase

1 reference

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Design, activity, and 2.8 A crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease

1 reference

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

1 reference

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Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution

1 reference

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

1 reference

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

1 reference

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Comparison of the refined crystal structures of liganded and unliganded chicken, yeast and trypanosomal triosephosphate isomerase

1 reference

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

1 reference

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12 December 2020

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inferred from PubMed ID database lookup

The structure of a synthetic pepsin inhibitor complexed with endothiapepsin

1 reference

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High-resolution structure of the complex between carboxypeptidase A andL-phenyl lactate

1 reference

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STUDIES ON THE ACTIVE CENTER OF TRYPSIN. THE BINDING OF AMIDINES AND GUANIDINES AS MODELS OF THE SUBSTRATE SIDE CHAIN

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Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins.

1 reference

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12 December 2020

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Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics

1 reference

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

1 reference

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12 December 2020

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inferred from PubMed ID database lookup

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

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Areas, volumes, packing and protein structure

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Electron paramagnetic resonance detectable states of cytochrome P-450cam

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. II. The binding of the pancreatic trypsin inhibitor and of isoleucine-valine and of sequentially related peptides to trypsinogen and to p-guanidinobenzoate-tryp

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Engineered interdomain disulfide in the periplasmic receptor for sulfate transport reduces flexibility. Site-directed mutagenesis and ligand-binding studies

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structure of the complex between carboxypeptidase A and the biproduct analog inhibitor l-benzylsuccinate at 2·0 Å resolution

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Classical electrostatics in biology and chemistry

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Use of binding energy in catalysis analyzed by mutagenesis of the tyrosyl-tRNA synthetase.

1 reference

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based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Acetylcholine binding by a synthetic receptor: implications for biological recognition

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enthalpy of hydrogen bond formation in a protein-ligand binding reaction

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystallographic refinement of human serum retinol binding protein at 2A resolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

pH profiles and isotope effects for aconitases from Saccharomycopsis lipolytica, beef heart, beef liver. .alpha.-Methyl-cis-aconitate and threo-Ds-.alpha.-methylisocitrate as substrates

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

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based on heuristic

inferred from PubMed ID database lookup

Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Protein Data Bank: a computer-based archival file for macromolecular structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

De novo design of enzyme inhibitors by Monte Carlo ligand generation

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV-1 protease

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydrogen bonding and biological specificity analysed by protein engineering

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Current methods for site-directed structure generation.

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of the structures of three carboxypeptidase A-phosphonate complexes determined by X-ray crystallography

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure-based discovery of inhibitors of thymidylate synthase

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Design of inhibitors of glycogen phosphorylase: a study of alpha- and beta-C-glucosides and 1-thio-beta-D-glucose compounds

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The binding of the retro-analogue of glutathione disulfide to glutathione reductase

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A strategy for theoretical binding constant, Ki, calculations for neuraminidase aromatic inhibitors designed on the basis of the active site structure of influenza virus neuraminidase.

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system.

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Reactivity of ferric Aplysia and sperm whale myoglobins towards imidazole

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Irreversible Enzyme Inhibitors. CVI.1 Proteolytic Enzymes. I. Bulk Tolerances in Trypsin-Inhibitor Complexes2

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A comparison of the structures of apo dogfish M4 lactate dehydrogenase and its ternary complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Orientational sampling and rigid-body minimization in molecular docking

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

CGP 38 560: orally active, low-molecular-weight renin inhibitor with high potency and specificity

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Expression of rat intestinal fatty acid-binding protein in Escherichia coli. Purification and comparison of ligand binding characteristics with that of Escherichia coli-derived rat liver fatty acid-binding protein

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Domain flexibility in aspartic proteinases

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

INTERACTION OF AROMATIC COMPOUNDS WITH ALPHA-CHYMOTRYPSIN

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Geometry of binding of the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural comparison of sulfodiimine and sulfonamide inhibitors in their complexes with zinc enzymes

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Design of enzyme inhibitors using iterative protein crystallographic analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Calculation of the free energy of association for protein complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Prediction of new serine proteinase inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Rates of ligand binding to periplasmic proteins involved in bacterial transport and chemotaxis

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate

1 reference

https://pubmed.ncbi.nlm.nih.gov/9777490

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1023/A:1007999920146

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journals/jcamd/Bohm98

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DBLP Dataset 2021-01-02

28 January 2021

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Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

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Consolidated OpenCitations Corpus – April 2017

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