(Q53678858)

English

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

scientific article published in September 1997

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. (English)

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

author name string

M D Eldridge

1

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

C W Murray

2

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

T R Auton

3

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

G V Paolini

4

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

R P Mee

5

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

publication date

1 September 1997

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

Journal of Computer - Aided Molecular Design

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

11

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

5

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

425-445

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

https://scigraph.springernature.com/pub.10.1023/a:1007996124545

0 references

Hydroxyethylene isostere inhibitors of human immunodeficiency virus-1 protease: structure-activity analysis using enzyme kinetics, X-ray crystallography, and infected T-cell assays

1 reference

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Structure of human neutrophil collagenase reveals large S1' specificity pocket

1 reference

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Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution

1 reference

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Molecular basis of crossreactivity and the limits of antibody-antigen complementarity

1 reference

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Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design

1 reference

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

1 reference

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Local and transmitted conformational changes on complexation of an anti-sweetener Fab

1 reference

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A new method for predicting binding affinity in computer-aided drug design

1 reference

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Analyses of ligand binding in five endothiapepsin crystal complexes and their use in the design and evaluation of novel renin inhibitors

1 reference

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

1 reference

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Recognition of a Cell-Surface Oligosaccharide of Pathogenic Salmonella by an Antibody Fab Fragment

1 reference

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Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution

1 reference

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X-ray crystallographic studies of a series of penicillin-derived asymmetric inhibitors of HIV-1 protease

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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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

https://pubmed.ncbi.nlm.nih.gov/9385547

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

1 reference

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12 December 2020

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X-ray crystallographic analysis of inhibition of endothiapepsin by cyclohexyl renin inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations

1 reference

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12 December 2020

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Binding of N-carboxymethyl dipeptide inhibitors to thermolysin determined by X-ray crystallography: a novel class of transition-state analogues for zinc peptidases

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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Principles and pitfalls in designing site-directed peptide ligands

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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Calculation of relative binding affinities of purine nucleoside phosphorylase inhibitors

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

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

High resolution X-ray analyses of renin inhibitor-aspartic proteinase complexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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Electron paramagnetic resonance detectable states of cytochrome P-450cam

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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Influenza B virus neuraminidase can synthesize its own inhibitor

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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

1 reference

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity

1 reference

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A Pro to Gly mutation in the hinge of the arabinose-binding protein enhances binding and alters specificity. Sugar-binding and crystallographic studies

1 reference

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

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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/9385547

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Hydrogen bonding and biological specificity analysed by protein engineering

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution

1 reference

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

1 reference

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Relocating a negative charge in the binding pocket of trypsin

1 reference

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Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin

1 reference

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A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

1 reference

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

1 reference

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CNAD: a potent and specific inhibitor of alcohol dehydrogenase

1 reference

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

1 reference

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High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme

1 reference

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Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism

1 reference

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Prediction of drug binding affinities by comparative binding energy analysis.

1 reference

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A check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor

1 reference

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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

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Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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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/9385547

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based on heuristic

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A fast flexible docking method using an incremental construction algorithm.

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

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Binding of hydroxamic acid inhibitors to crystalline thermolysin suggests a pentacoordinate zinc intermediate in catalysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

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Crystallographic structural analysis of phosphoramidates as inhibitors and transition-state analogs of thermolysin

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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based on heuristic

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Structure-based understanding of ligand affinity using human thrombin as a model system

1 reference

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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/9385547

12 December 2020

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

1 reference

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Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase

1 reference

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Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

1 reference

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12 December 2020

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Direct observation by X‐ray analysis of the tetrahedral “intermediate” of aspartic proteinases

1 reference

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Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution

1 reference

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1 reference

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PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology

1 reference

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

1 reference

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12 December 2020

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Dehydrogenase binding by tiazofurin anabolites.

1 reference

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12 December 2020

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Conformational changes of small molecules binding to proteins

1 reference

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12 December 2020

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Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

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/9385547

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/9385547

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Major enhancement of the affinity of an enzyme for a transition-state analog by a single hydroxyl group

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Refined 1.89-A structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A relationship between protein stability and protein function

1 reference

https://pubmed.ncbi.nlm.nih.gov/9385547

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1023/A:1007996124545

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

DBLP publication ID

journals/jcamd/EldridgeMAPM97

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

17 May 2018

http://europepmc.org/abstract/MED/9385547

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