| nr |
titel |
auteur |
tijdschrift |
jaar |
jaarg. |
afl. |
pagina('s) |
type |
| 1 |
A Comparative Molecular Similarity Index Analysis (CoMSIA) study identifies an HLA-A2 binding supermotif
|
Irini A. Doytchinova
|
|
2002
|
|
8 |
p. 535-544
10 p.
|
artikel
|
| 2 |
A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP
|
Yogendra Patel
|
|
2002
|
|
8 |
p. 653-681
29 p.
|
artikel
|
| 3 |
A computational analysis of the binding model of MDM2 with inhibitors
|
Hu, Guodong
|
|
2010
|
|
8 |
p. 687-697
|
artikel
|
| 4 |
Active site similarity between human and Plasmodium falciparum phosphodiesterases: considerations for antimalarial drug design
|
Howard, Brittany L.
|
|
2011
|
|
8 |
p. 753-762
|
artikel
|
| 5 |
A grand vision for configurable science and minimizing the loss model
|
Warr, Wendy A.
|
|
2008
|
|
8 |
p. 587-591
|
artikel
|
| 6 |
Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1
|
Bhattacharya, Supriyo
|
|
2010
|
|
8 |
p. 659-674
|
artikel
|
| 7 |
Analysis of stacking overlap in nucleic acid structures: algorithm and application
|
Pingali, Pavan Kumar
|
|
2014
|
|
8 |
p. 851-867
|
artikel
|
| 8 |
A new topological index to elucidate apolar hydrocarbons
|
Francisco Torrens
|
|
2001
|
|
8 |
p. 709-719
11 p.
|
artikel
|
| 9 |
A pharmacophore model for dopamine D4 receptor antagonists
|
Jonas Boström
|
|
2000
|
|
8 |
p. 769-786
18 p.
|
artikel
|
| 10 |
Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition
|
Jedwabny, Wiktoria
|
|
2017
|
|
8 |
p. 715-728
|
artikel
|
| 11 |
A QM/MM study of the binding of RAPTA ligands to cathepsin B
|
Ciancetta, Antonella
|
|
2011
|
|
8 |
p. 729-742
|
artikel
|
| 12 |
ART–RRT: As-Rigid-As-Possible search for protein conformational transition paths
|
Nguyen, Minh Khoa
|
|
2019
|
|
8 |
p. 705-727
|
artikel
|
| 13 |
A theoretical study of cis–trans isomerisation in H-ZSM5: probing the impact of cluster size and zeolite framework on energetics and structure
|
Gleeson, Duangkamol
|
|
2008
|
|
8 |
p. 579-585
|
artikel
|
| 14 |
Automated computational screening of the thiol reactivity of substituted alkenes
|
Smith, Jennifer M.
|
|
2015
|
|
8 |
p. 725-735
|
artikel
|
| 15 |
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
|
Robin J. Rosenfeld
|
|
2003
|
|
8 |
p. 525-536
12 p.
|
artikel
|
| 16 |
Automated molecule editing in molecular design
|
Kenny, Peter W.
|
|
2013
|
|
8 |
p. 655-664
|
artikel
|
| 17 |
Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules
|
Arroyuelo, Agustina
|
|
2016
|
|
8 |
p. 619-624
|
artikel
|
| 18 |
Benzimidazole derivatives. 4. The recognition of the voluminous substituent attached to the basic amino group of 5-HT4 receptor antagonists
|
María L. López-Rodríguez
|
|
2003
|
|
8 |
p. 515-524
10 p.
|
artikel
|
| 19 |
Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning
|
Tanoori, Betsabeh
|
|
|
|
8 |
p. 883-900
|
artikel
|
| 20 |
Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR
|
Westermaier, Yvonne
|
|
2017
|
|
8 |
p. 755-775
|
artikel
|
| 21 |
Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds
|
Marrero-Ponce, Yovani
|
|
2008
|
|
8 |
p. 523-540
|
artikel
|
| 22 |
Box size effects are negligible for solvation free energies of neutral solutes
|
Parameswaran, Sreeja
|
|
2014
|
|
8 |
p. 825-829
|
artikel
|
| 23 |
Challenges of fragment screening
|
Joseph-McCarthy, Diane
|
|
2009
|
|
8 |
p. 449-451
|
artikel
|
| 24 |
Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray alignment
|
Wendt, Bernd
|
|
2014
|
|
8 |
p. 803-824
|
artikel
|
| 25 |
Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach
|
Paciotti, Roberto
|
|
|
|
8 |
p. 897-914
|
artikel
|
| 26 |
Chemical space networks: a powerful new paradigm for the description of chemical space
|
Maggiora, Gerald M.
|
|
2014
|
|
8 |
p. 795-802
|
artikel
|
| 27 |
Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules
|
Xu, Liang
|
|
2012
|
|
8 |
p. 963-976
|
artikel
|
| 28 |
Combining fragment homology modeling with molecular dynamics aims at prediction of Ca2+ binding sites in CaBPs
|
Pang, ChunLi
|
|
2013
|
|
8 |
p. 697-705
|
artikel
|
| 29 |
Comprehensive model of wild-type and mutant HIV-1 reverse transciptases
|
Ballante, Flavio
|
|
2012
|
|
8 |
p. 907-919
|
artikel
|
| 30 |
Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization
|
Carl D. Elkin
|
|
2000
|
|
8 |
p. 705-718
14 p.
|
artikel
|
| 31 |
Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site
|
Oguievetskaia, Ksenia
|
|
2009
|
|
8 |
p. 571-582
|
artikel
|
| 32 |
Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators
|
Wang, Huiqun
|
|
|
|
8 |
p. 879-895
|
artikel
|
| 33 |
Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds
|
Cheng, Mary Hongying
|
|
2008
|
|
8 |
p. 563-570
|
artikel
|
| 34 |
Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl–ThDP
|
Alvarado, Omar
|
|
2012
|
|
8 |
p. 977-982
|
artikel
|
| 35 |
Conformational analysis of kainate in aqueous solution in relation to its binding to AMPA and kainic acid receptors
|
Peter Aadal Nielsen
|
|
2001
|
|
8 |
p. 753-763
11 p.
|
artikel
|
| 36 |
Conformational ensemble comparison for small molecules in drug discovery
|
Habgood, Matthew
|
|
2018
|
|
8 |
p. 841-852
|
artikel
|
| 37 |
Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its C-atom coordinates
|
Paul A.M. van Hooft
|
|
2000
|
|
8 |
p. 719-730
12 p.
|
artikel
|
| 38 |
Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics
|
Roumen, Luc
|
|
2007
|
|
8 |
p. 455-471
|
artikel
|
| 39 |
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge
|
Diedenhofen, Michael
|
|
|
|
8 |
p. 395-405
|
artikel
|
| 40 |
Covalent docking in CDOCKER
|
Wu, Yujin
|
|
|
|
8 |
p. 563-574
|
artikel
|
| 41 |
Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex
|
Praditwongwan, Warachai
|
|
2014
|
|
8 |
p. 869-884
|
artikel
|
| 42 |
Cyclodextrin knowledgebase a web-based service managing CD-ligand complexation data
|
Hazai, Eszter
|
|
2010
|
|
8 |
p. 713-717
|
artikel
|
| 43 |
Deciphering common failures in molecular docking of ligand-protein complexes
|
Gennady M. Verkhivker
|
|
2000
|
|
8 |
p. 731-751
21 p.
|
artikel
|
| 44 |
Demystifying the pH dependent conformational changes of human heparanase pertaining to structure–function relationships: an in silico approach
|
Nagarajan, Hemavathy
|
|
2018
|
|
8 |
p. 821-840
|
artikel
|
| 45 |
Dependency of ligand free energy landscapes on charge parameters and solvent models
|
Okamoto, Yuko
|
|
2010
|
|
8 |
p. 699-712
|
artikel
|
| 46 |
Design of a colicin E7 based chimeric zinc-finger nuclease
|
Németh, Eszter
|
|
2014
|
|
8 |
p. 841-850
|
artikel
|
| 47 |
Design of compound libraries for fragment screening
|
Blomberg, Niklas
|
|
2009
|
|
8 |
p. 513-525
|
artikel
|
| 48 |
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions
|
Delaunay, Maxence
|
|
|
|
8 |
p. 605-621
|
artikel
|
| 49 |
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase
|
Landon, Melissa R.
|
|
2009
|
|
8 |
p. 491-500
|
artikel
|
| 50 |
Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint
|
Karabulut, Sedat
|
|
2013
|
|
8 |
p. 681-688
|
artikel
|
| 51 |
Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors
|
Gozalbes, Rafael
|
|
2009
|
|
8 |
p. 555-569
|
artikel
|
| 52 |
Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands
|
Nunzia Cinone
|
|
2000
|
|
8 |
p. 753-768
16 p.
|
artikel
|
| 53 |
Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase
|
Tran, Diem-Trang T.
|
|
2013
|
|
8 |
p. 689-695
|
artikel
|
| 54 |
Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study
|
Thai, Nguyen Quoc
|
|
2016
|
|
8 |
p. 639-650
|
artikel
|
| 55 |
3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors
|
Haregewein Assefa
|
|
2003
|
|
8 |
p. 475-493
19 p.
|
artikel
|
| 56 |
Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy
|
Teixeira, Olivia
|
|
|
|
8 |
p. 871-882
|
artikel
|
| 57 |
Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble
|
Yongye, Austin B.
|
|
2010
|
|
8 |
p. 675-686
|
artikel
|
| 58 |
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
|
Loving, Kathryn
|
|
2009
|
|
8 |
p. 541-554
|
artikel
|
| 59 |
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge
|
Ali, Hafiz Saqib
|
|
|
|
8 |
p. 911-921
|
artikel
|
| 60 |
ENPDA: an evolutionary structure-based de novo peptide design algorithm
|
Belda, Ignasi
|
|
2005
|
|
8 |
p. 585-601
|
artikel
|
| 61 |
Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
|
Shirts, Michael R.
|
|
2017
|
|
8 |
p. 777
|
artikel
|
| 62 |
Estimation of the size of drug-like chemical space based on GDB-17 data
|
Polishchuk, P. G.
|
|
2013
|
|
8 |
p. 675-679
|
artikel
|
| 63 |
Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships
|
Miyao, Tomoyuki
|
|
2019
|
|
8 |
p. 729-743
|
artikel
|
| 64 |
Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation
|
Wright, James S.
|
|
2013
|
|
8 |
p. 707-721
|
artikel
|
| 65 |
Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach
|
Sixto-López, Yudibeth
|
|
|
|
8 |
p. 857-878
|
artikel
|
| 66 |
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES
|
Bjerrum, Esben Jannik
|
|
|
|
8 |
p. 373-394
|
artikel
|
| 67 |
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study
|
Albert Salichs
|
|
2002
|
|
8 |
p. 569-583
15 p.
|
artikel
|
| 68 |
Fragment-based drug discovery
|
Warr, Wendy A.
|
|
2009
|
|
8 |
p. 453-458
|
artikel
|
| 69 |
Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology
|
Neumann, Lars
|
|
2009
|
|
8 |
p. 501-511
|
artikel
|
| 70 |
FRED and HYBRID docking performance on standardized datasets
|
McGann, Mark
|
|
2012
|
|
8 |
p. 897-906
|
artikel
|
| 71 |
Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities
|
Dolenc, Jožica
|
|
2011
|
|
8 |
p. 709-716
|
artikel
|
| 72 |
Generating conformational transition paths with low potential-energy barriers for proteins
|
Nguyen, Minh Khoa
|
|
2018
|
|
8 |
p. 853-867
|
artikel
|
| 73 |
Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening
|
Schlegel, Birgit
|
|
2007
|
|
8 |
p. 437-453
|
artikel
|
| 74 |
Genetic algorithm for the design of molecules with desired properties
|
Stefan Kamphausen
|
|
2002
|
|
8 |
p. 551-567
17 p.
|
artikel
|
| 75 |
H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection
|
Ebina, Teppei
|
|
2014
|
|
8 |
p. 831-839
|
artikel
|
| 76 |
How computational chemistry develops: a tribute to Peter Goodford
|
Cruciani, Gabriele
|
|
2019
|
|
8 |
p. 699-703
|
artikel
|
| 77 |
How medicinal chemists learned about log P
|
Martin, Yvonne Connolly
|
|
2018
|
|
8 |
p. 809-819
|
artikel
|
| 78 |
HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data
|
Carrillo-Tripp, Mauricio
|
|
2018
|
|
8 |
p. 869-876
|
artikel
|
| 79 |
Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates: a 3D-QSAR study
|
Fernández, David
|
|
2013
|
|
8 |
p. 739-754
|
artikel
|
| 80 |
Identification of common inhibitors of wild-type and T315I mutant of BCR-ABL through the parallel structure-based virtual screening
|
Park, Hwangseo
|
|
2012
|
|
8 |
p. 983-992
|
artikel
|
| 81 |
Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants
|
Joaquim Mendes
|
|
2001
|
|
8 |
p. 721-740
20 p.
|
artikel
|
| 82 |
Improved convergence of binding affinities with free energy perturbation: Application to nonpeptide ligands with pp60src SH2 domain
|
Daniel J. Price
|
|
2001
|
|
8 |
p. 681-695
15 p.
|
artikel
|
| 83 |
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015
|
Xu, Xianjin
|
|
2017
|
|
8 |
p. 689-699
|
artikel
|
| 84 |
Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension
|
Armstrong, M. Stuart
|
|
2011
|
|
8 |
p. 785-790
|
artikel
|
| 85 |
Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field method
|
Soni, Anjali
|
|
|
|
8 |
p. 817-830
|
artikel
|
| 86 |
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level
|
García-Marín, Javier
|
|
|
|
8 |
p. 575-589
|
artikel
|
| 87 |
Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies
|
Simeon, Saw
|
|
2019
|
|
8 |
p. 745-757
|
artikel
|
| 88 |
In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases
|
Eberini, Ivano
|
|
2011
|
|
8 |
p. 743-752
|
artikel
|
| 89 |
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease
|
Varikoti, Rohith Anand
|
|
|
|
8 |
p. 339-355
|
artikel
|
| 90 |
Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling
|
Rácz, Anita
|
|
|
|
8 |
p. 831-839
|
artikel
|
| 91 |
Lessons for fragment library design: analysis of output from multiple screening campaigns
|
Chen, I-Jen
|
|
2009
|
|
8 |
p. 603-620
|
artikel
|
| 92 |
Ligand- and receptor-based docking with LiBELa
|
Santos Muniz, Heloisa dos
|
|
2015
|
|
8 |
p. 713-723
|
artikel
|
| 93 |
Many InChIs and quite some feat
|
Warr, Wendy A.
|
|
2015
|
|
8 |
p. 681-694
|
artikel
|
| 94 |
Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design
|
Lättig, Jens
|
|
2007
|
|
8 |
p. 473-483
|
artikel
|
| 95 |
Metal complexes of chiral pentaazacrowns as conformational templates for -turn recognition
|
Andrea J.H. Reaka
|
|
2002
|
|
8 |
p. 585-600
16 p.
|
artikel
|
| 96 |
Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations
|
Cui, Meng
|
|
2008
|
|
8 |
p. 553-561
|
artikel
|
| 97 |
Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information
|
Paoletta, Silvia
|
|
2015
|
|
8 |
p. 737-756
|
artikel
|
| 98 |
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors
|
Zhu, Kai
|
|
|
|
8 |
p. 591-604
|
artikel
|
| 99 |
Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors
|
Teixeira, Cátia
|
|
2011
|
|
8 |
p. 763-775
|
artikel
|
| 100 |
Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase
|
Perdih, Andrej
|
|
2013
|
|
8 |
p. 723-738
|
artikel
|
| 101 |
Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A)
|
Hyunmyung Kim
|
|
2002
|
|
8 |
p. 601-610
10 p.
|
artikel
|
| 102 |
Molecular dynamics to enhance structure-based virtual screening on cathepsin B
|
Ogrizek, Mitja
|
|
2015
|
|
8 |
p. 707-712
|
artikel
|
| 103 |
Molecular graph convolutions: moving beyond fingerprints
|
Kearnes, Steven
|
|
2016
|
|
8 |
p. 595-608
|
artikel
|
| 104 |
mRAISE: an alternative algorithmic approach to ligand-based virtual screening
|
Behren, Mathias M. von
|
|
2016
|
|
8 |
p. 583-594
|
artikel
|
| 105 |
Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge
|
Lopez, Kenneth
|
|
|
|
8 |
p. 923-931
|
artikel
|
| 106 |
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge
|
Lenselink, Eelke B.
|
|
|
|
8 |
p. 901-909
|
artikel
|
| 107 |
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules
|
Stroet, Martin
|
|
|
|
8 |
p. 357-371
|
artikel
|
| 108 |
Open3DALIGN: an open-source software aimed at unsupervised ligand alignment
|
Tosco, Paolo
|
|
2011
|
|
8 |
p. 777-783
|
artikel
|
| 109 |
Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
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Kim, Ki Hwan
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