(Q47396241)

15 January 2018

title

Ligand-supported Homology Modelling of Protein Binding-sites using Knowledge-based Potentials (English)

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https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

30 March 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14607122

30 March 2024

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

30 March 2024

author name string

Andreas Evers

1

1 reference

15 January 2018

Holger Gohlke

2

1 reference

15 January 2018

Gerhard Klebe

3

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15 January 2018

language of work or name

English

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publication date

1 November 2003

1 reference

15 January 2018

21 November 2003

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=14607122

full work available at URL

30 March 2024

number of pages

19

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based on heuristic

inferred from page(s)

https://api.elsevier.com/content/article/PII:S0022283603011884?httpAccept=text/xml

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https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

https://api.elsevier.com/content/article/PII:S0022283603011884?httpAccept=text/plain

30 March 2024

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https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Journal of Molecular Biology

30 March 2024

published in

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15 January 2018

volume

334

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15 January 2018

issue

2

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15 January 2018

page(s)

327-345

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15 January 2018

Initial sequencing and analysis of the human genome

cites work

1 reference

28 May 2022

https://opencitations.net/index/coci/api/v1/citations/10.1038/35057062

Detecting protein function and protein-protein interactions from genome sequences

1

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium

30 March 2024

2

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Comparative genomics of the eukaryotes

30 March 2024

4

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Protein structure modeling for structural genomics.

30 March 2024

5

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Target selection for structural genomics

30 March 2024

6

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Expectations from structural genomics

30 March 2024

7

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Mapping the protein universe

30 March 2024

8

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Comparative protein structure modeling of genes and genomes

30 March 2024

9

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Analysis and assessment of comparative modeling predictions in CASP4.

30 March 2024

10

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Comparison of performance in successive CASP experiments.

30 March 2024

12

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

30 March 2024

13

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Protein folds, functions and evolution

30 March 2024

14

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

From structure to function: approaches and limitations

30 March 2024

15

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Structural genomics and its importance for gene function analysis.

30 March 2024

16

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Automated genome sequence analysis and annotation

30 March 2024

17

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

New roles for structure in biology and drug discovery

30 March 2024

18

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Drug design strategies for targeting G-protein-coupled receptors

30 March 2024

19

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Modelling of the binding site of the human m1 muscarinic receptor: experimental validation and refinement

30 March 2024

20

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ.

30 March 2024

21

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2)

30 March 2024

22

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase

30 March 2024

23

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands.

30 March 2024

24

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Models of the extracellular domain of the nicotinic receptors and of agonist- and Ca2+-binding sites

30 March 2024

25

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors.

30 March 2024

26

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Peptide/benzodiazepine hybrids as ligands of CCKA and CCKB receptors

30 March 2024

27

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Regioselectivity of CYP2B6: homology modeling, molecular dynamics simulation, docking

30 March 2024

28

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Computational model of the complex between GR113808 and the 5-HT4 receptor guided by site-directed mutagenesis and the crystal structure of rhodopsin

30 March 2024

29

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets?

30 March 2024

30

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Prediction of structure and function of G protein-coupled receptors

30 March 2024

31

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A New Approach to Docking in the β2-Adrenergic Receptor That Exploits the Domain Structure of G-Protein-Coupled Receptors

30 March 2024

32

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Molecular modeling studies of human A3 adenosine antagonists: structural homology and receptor docking

30 March 2024

33

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Human P2Y1 receptor: molecular modeling and site-directed mutagenesis as tools to identify agonist and antagonist recognition sites.

30 March 2024

34

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A three-dimensional construction of the active site (region 507-749) of human neutral endopeptidase (EC.3.4.24.11)

30 March 2024

35

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Molecular modeling of the interactions of glutamate carboxypeptidase II with its potent NAAG-based inhibitors

30 March 2024

36

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Homology modeling of gelatinase catalytic domains and docking simulations of novel sulfonamide inhibitors

30 March 2024

37

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Pseudo-receptor modeling: a new concept for the three-dimensional construction of receptor binding sites

30 March 2024

38

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Molecular design using the minireceptor concept

30 March 2024

39

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A novel modeling protocol for protein receptors guided by bound-ligand conformation.

30 March 2024

40

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Homology model directed alignment selection for comparative molecular field analysis: application to photosystem II inhibitors

30 March 2024

41

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Docking ligands onto binding site representations derived from proteins built by homology modelling.

30 March 2024

42

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines

30 March 2024

43

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction.

30 March 2024

44

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Principles of docking: An overview of search algorithms and a guide to scoring functions

30 March 2024

46

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Folding funnels and binding mechanisms

30 March 2024

47

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

48

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

49

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

50

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

51

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A novel computational tool for automated structure-based drug design

30 March 2024

52

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

53

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

54

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Different approaches toward an automatic structural alignment of drug molecules: applications to sterol mimics, thrombin and thermolysin inhibitors

30 March 2024

56

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Methodological developments and strategies for a fast flexible superposition of drug-size molecules

30 March 2024

57

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Molecular docking to ensembles of protein structures

30 March 2024

58

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

30 March 2024

59

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

FlexE: efficient molecular docking considering protein structure variations.

30 March 2024

60

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Empirical potentials and functions for protein folding and binding.

30 March 2024

61

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Structure-derived potentials and protein simulations

30 March 2024

62

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Perspectives in protein-fold recognition

30 March 2024

63

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Knowledge-based potentials for proteins

30 March 2024

64

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Knowledge-based scoring function to predict protein-ligand interactions.

30 March 2024

65

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

30 March 2024

68

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence

30 March 2024

69

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Docking into knowledge-based potential fields: a comparative evaluation of DrugScore

30 March 2024

71

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.

30 March 2024

72

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Comparative protein modelling by satisfaction of spatial restraints

30 March 2024

73

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Modeling of loops in protein structures

30 March 2024

74

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

30 March 2024

75

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

30 March 2024

76

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Verification of protein structures: patterns of nonbonded atomic interactions

30 March 2024

77

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Identifying native-like protein structures using physics-based potentials

30 March 2024

78

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Main-chain bond lengths and bond angles in protein structures

30 March 2024

80

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Assessment of protein models with three-dimensional profiles

30 March 2024

81

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Assessing protein structures with a non-local atomic interaction energy.

30 March 2024

82

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

30 March 2024

83

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

A new computational model for protein folding based on atomic solvation

30 March 2024

84

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Discriminating compact nonnative structures from the native structure of globular proteins

30 March 2024

85

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB

30 March 2024

86

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

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

30 March 2024

87

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Crystal structures of human factor Xa complexed with potent inhibitors

30 March 2024

89

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming

30 March 2024

90

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors

30 March 2024

91

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Optimization of the beta-aminoester class of factor Xa inhibitors. Part 2: Identification of FXV673 as a potent and selective inhibitor with excellent In vivo anticoagulant activity

30 March 2024

92

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Structural basis for chemical inhibition of human blood coagulation factor Xa

30 March 2024

93

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Preparation, characterization, and the crystal structure of the inhibitor ZK-807834 (CI-1031) complexed with factor Xa

30 March 2024

94

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition

30 March 2024

95

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Protein structure prediction in 2002.

30 March 2024

97

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Critical assessment of methods of protein structure prediction (CASP): round IV.

30 March 2024

98

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Generalized-ensemble algorithms for molecular simulations of biopolymers

30 March 2024

99

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Protein folding: the endgame

30 March 2024

101

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Protein sidechain conformer prediction: a test of the energy function

30 March 2024

102

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Extending the accuracy limits of prediction for side-chain conformations

30 March 2024

103

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design

30 March 2024

104

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Statistical thermodynamic linkage between conformational and binding equilibria.

30 March 2024

105

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

30 March 2024

106

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

Folding and binding cascades: shifts in energy landscapes

30 March 2024

107

1 reference

https://api.crossref.org/works/10.1016/J.JMB.2003.09.032

30 March 2024

Identifiers

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15 January 2018

1 reference

15 January 2018