Works matching IS 0920654X AND DT 2018 AND VI 32 AND IP 1

Results: 24

A cross docking pipeline for improving pose prediction and virtual screening performance.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 163, doi. 10.1007/s10822-017-0048-z

By:

Kumar, Ashutosh;
Zhang, Kam Y. J.

Publication type:

Article

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 175, doi. 10.1007/s10822-017-0049-y

By:

Kurkcuoglu, Zeynep;
Koukos, Panagiotis I.;
Citro, Nevia;
Trellet, Mikael E.;
Rodrigues, J. P. G. L. M.;
Moreira, Irina S.;
Roel-Touris, Jorge;
Melquiond, Adrien S. J.;
Geng, Cunliang;
Schaarschmidt, Jörg;
Xue, Li C.;
Vangone, Anna;
Bonvin, A. M. J. J.

Publication type:

Article

CDOCKER and $$\lambda$$ -dynamics for prospective prediction in D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 89, doi. 10.1007/s10822-017-0050-5

By:

Ding, Xinqiang;
Hayes, Ryan L.;
Vilseck, Jonah Z.;
Charles, Murchtricia K.;
Brooks, Charles L.

Publication type:

Article

Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 251, doi. 10.1007/s10822-017-0051-4

By:

Salmaso, Veronica;
Sturlese, Mattia;
Cuzzolin, Alberto;
Moro, Stefano

Publication type:

Article

Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 113, doi. 10.1007/s10822-017-0053-2

By:

Fradera, Xavier;
Verras, Andreas;
Hu, Yuan;
Wang, Deping;
Wang, Hongwu;
Fells, James I.;
Armacost, Kira A.;
Crespo, Alejandro;
Sherborne, Brad;
Wang, Huijun;
Peng, Zhengwei;
Gao, Ying-Duo

Publication type:

Article

Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 273, doi. 10.1007/s10822-017-0054-1

By:

Selwa, Edithe;
Elisée, Eddy;
Zavala, Agustin;
Iorga, Bogdan I.

Publication type:

Article

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 239, doi. 10.1007/s10822-017-0055-0

By:

Rifai, Eko Aditya;
van Dijk, Marc;
Vermeulen, Nico P. E.;
Geerke, Daan P.

Publication type:

Article

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 211, doi. 10.1007/s10822-017-0056-z

By:

Olsson, Martin A.;
García-Sosa, Alfonso T.;
Ryde, Ulf

Publication type:

Article

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 187, doi. 10.1007/s10822-017-0058-x

By:

Lam, Polo C.-H.;
Abagyan, Ruben;
Totrov, Maxim

Publication type:

Article

Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 151, doi. 10.1007/s10822-017-0062-1

By:

Kadukova, Maria;
Grudinin, Sergei

Publication type:

Article

Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 231, doi. 10.1007/s10822-017-0063-0

By:

Réau, Manon;
Langenfeld, Florent;
Zagury, Jean-François;
Montes, Matthieu

Publication type:

Article

Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 265, doi. 10.1007/s10822-017-0064-z

By:

Schindler, Christina;
Rippmann, Friedrich;
Kuhn, Daniel

Publication type:

Article

Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 287, doi. 10.1007/s10822-017-0065-y

By:

Wingert, Bentley M.;
Oerlemans, Rick;
Camacho, Carlos J.

Publication type:

Article

Protein-ligand docking using FFT based sampling: D3R case study.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 225, doi. 10.1007/s10822-017-0069-7

By:

Padhorny, Dzmitry;
Hall, David R.;
Mirzaei, Hanieh;
Mamonov, Artem B.;
Moghadasi, Mohammad;
Alekseenko, Andrey;
Beglov, Dmitri;
Kozakov, Dima

Publication type:

Article

Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 143, doi. 10.1007/s10822-017-0071-0

By:

Hogues, Hervé;
Sulea, Traian;
Gaudreault, Francis;
Corbeil, Christopher R.;
Purisima, Enrico O.

Publication type:

Article

Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 129, doi. 10.1007/s10822-017-0072-z

By:

Gao, Ying-Duo;
Hu, Yuan;
Crespo, Alejandro;
Wang, Deping;
Armacost, Kira A.;
Fells, James I.;
Fradera, Xavier;
Wang, Hongwu;
Wang, Huijun;
Sherborne, Brad;
Verras, Andreas;
Peng, Zhengwei

Publication type:

Article

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 59, doi. 10.1007/s10822-017-0074-x

By:

Bhakat, Soumendranath;
Åberg, Emil;
Söderhjelm, Pär

Publication type:

Article

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 21, doi. 10.1007/s10822-017-0075-9

By:

Athanasiou, Christina;
Vasilakaki, Sofia;
Dellis, Dimitris;
Cournia, Zoe

Publication type:

Article

Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 45, doi. 10.1007/s10822-017-0081-y

By:

Baumgartner, Matthew P.;
Evans, David A.

Publication type:

Article

Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 103, doi. 10.1007/s10822-017-0082-x

By:

Duan, Rui;
Xu, Xianjin;
Zou, Xiaoqin

Publication type:

Article

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 199, doi. 10.1007/s10822-017-0083-9

By:

Mey, Antonia S. J. S.;
Jiménez, Jordi Juárez;
Michel, Julien

Publication type:

Article

Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 299, doi. 10.1007/s10822-017-0085-7

By:

Yakovenko, Oleksandr;
Jones, Steven J. M.

Publication type:

Article

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 1, doi. 10.1007/s10822-017-0088-4

By:

Gaieb, Zied;
Liu, Shuai;
Gathiaka, Symon;
Chiu, Michael;
Yang, Huanwang;
Shao, Chenghua;
Feher, Victoria A.;
Walters, W. Patrick;
Kuhn, Bernd;
Rudolph, Markus G.;
Burley, Stephen K.;
Gilson, Michael K.;
Amaro, Rommie E.

Publication type:

Article

Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2.

Published in:

Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 75, doi. 10.1007/s10822-017-0046-1

By:

da Silva Figueiredo Celestino Gomes, Priscila;
Da Silva, Franck;
Bret, Guillaume;
Rognan, Didier

Publication type:

Article