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ORCIDJournal of Computer-Aided Molecular Design, Volume 32
Volume 32, Number 1, January 2018
- Zied Gaieb, Shuai Liu, Symon Gathiaka, Michael Chiu
, Huanwang Yang, Chenghua Shao, Victoria A. Feher, W. Patrick Walters, Bernd Kuhn, Markus G. Rudolph, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro:
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. 1-20 - Christina Athanasiou, Sofia Vasilakaki, Dimitris Dellis, Zoe Cournia:
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. 21-44 - Matthew P. Baumgartner, David A. Evans:
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2. 45-58 - Soumendranath Bhakat, Emil Åberg, Pär Söderhjelm:
Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling. 59-73 - Priscila da Silva Figueiredo Celestino Gomes, Franck Da Silva, Guillaume Bret, Didier Rognan:
Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2. 75-87 - Xinqiang Ding, Ryan L. Hayes, Jonah Z. Vilseck, Murchtricia K. Charles, Charles L. Brooks III:
CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2. 89-102 - Rui Duan, Xianjin Xu, Xiaoqin Zou:
Lessons learned from participating in D3R 2016 Grand Challenge 2: compounds targeting the farnesoid X receptor. 103-111 - Xavier Fradera, Andreas Verras, Yuan Hu, Deping Wang, Hongwu Wang, James I. Fells, Kira A. Armacost, Alejandro Crespo, Brad Sherborne, Huijun Wang, Zhengwei Peng, Ying-Duo Gao:
Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016. 113-127 - Ying-Duo Gao, Yuan Hu, Alejandro Crespo, Deping Wang, Kira A. Armacost, James I. Fells, Xavier Fradera, Hongwu Wang, Huijun Wang, Brad Sherborne, Andreas Verras, Zhengwei Peng:
Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort. 129-142 - Hervé Hogues, Traian Sulea, Francis Gaudreault, Christopher R. Corbeil, Enrico O. Purisima:
Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method. 143-150 - Maria Kadukova, Sergei Grudinin:
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2. 151-162 - Ashutosh Kumar, Kam Y. J. Zhang:
A cross docking pipeline for improving pose prediction and virtual screening performance. 163-173 - Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, Alexandre M. J. J. Bonvin:
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. 175-185 - Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov:
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. 187-198 - Antonia S. J. S. Mey, Jordi Juárez Jiménez, Julien Michel:
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations. 199-210 - Martin A. Olsson, Alfonso T. García-Sosa, Ulf Ryde:
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. 211-224 - Dzmitry Padhorny, David R. Hall, Hanieh Mirzaei, Artem B. Mamonov, Mohammad Moghadasi, Andrey Alekseenko, Dmitri Beglov, Dima Kozakov:
Protein-ligand docking using FFT based sampling: D3R case study. 225-230 - Manon Réau, Florent Langenfeld, Jean-François Zagury, Matthieu Montès:
Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study. 231-238 - Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Daan P. Geerke:
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. 239-249 - Veronica Salmaso, Mattia Sturlese, Alberto Cuzzolin, Stefano Moro:
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2. 251-264 - Christina E. M. Schindler, Friedrich Rippmann, Daniel Kuhn:
Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+. 265-272 - Edithe Selwa, Eddy Elisée, Agustin Zavala, Bogdan I. Iorga:
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations. 273-286 - Bentley M. Wingert, Rick Oerlemans, Carlos J. Camacho:
Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. 287-297 - Oleksandr Yakovenko, Steven J. M. Jones:
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. 299-311
Volume 32, Number 2, February 2018
- Johann Gasteiger, Yvonne C. Martin, Anthony Nicholls, Tudor I. Oprea, Terry R. Stouch:
Leaving us with fond memories, smiles, SMILES and, alas, tears: a tribute to David Weininger, 1952-2016. 313-319 - Ryo Kunimoto, Jürgen Bajorath:
Design of a tripartite network for the prediction of drug targets. 321-330 - Zoltán Orgován, György G. Ferenczy, Thomas Steinbrecher, Bence Szilágyi, Dávid Bajusz, György M. Keserü:
Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors. 331-345 - Miao Yu, Qiong Gu, Jun Xu:
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening. 347-361 - Natalia Nikitina, Evgeny Ivashko, Andrei Tchernykh:
Congestion game scheduling for virtual drug screening optimization. 363-374 - Mohammad Amin Valizade Hasanloei, Razieh Sheikhpour, Mehdi Agha Sarram, Elnaz Sheikhpour, Hamdollah Sharifi:
A combined Fisher and Laplacian score for feature selection in QSAR based drug design using compounds with known and unknown activities. 375-384 - Stefano Della-Longa, Alessandro Arcovito:
"In silico" study of the binding of two novel antagonists to the nociceptin receptor. 385-400
Volume 32, Number 3, March 2018
- Timur Gimadiev, Timur I. Madzhidov, Ramil I. Nugmanov, Igor I. Baskin, Igor S. Antipin, Alexandre Varnek:
Assessment of tautomer distribution using the condensed reaction graph approach. 401-414 - Sebastian Raschka, Anne M. Scott, Nan Liu, Santosh Gunturu, Mar Huertas, Weiming Li, Leslie A. Kuhn:
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control. 415-433 - Manuela Sabatino, Dante Rotili, Alexandros Patsilinakos, Mariantonietta Forgione, Daniela Tomaselli, Fréderic Alby, Paola B. Arimondo, Antonello Mai, Rino Ragno:
Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. 435-458 - Zainab K. Sanusi, Thavendran Govender, Glenn E. M. Maguire, Sibusiso B. Maseko, Johnson Lin, Hendrik G. Kruger, Bahareh Honarparvar:
An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. 459-471 - Stefania Villa, Laura Legnani, Diego Colombo, Arianna Gelain, Carmen Lammi, Daniele Bongiorno, Denise P. Ilboudo, Kellen E. McGee, Jürgen Bosch, Giovanni Grazioso:
Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors. 473-486 - Krishna P. Singh, Lokesh Baweja, Olaf Wolkenhauer, Qamar Rahman, Shailendra K. Gupta:
Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide. 487-496
Volume 32, Number 4, April 2018
- David A. Winkler:
Sparse QSAR modelling methods for therapeutic and regenerative medicine. 497-509 - Sebastian Raschka, Alex J. Wolf, Joseph Bemister-Buffington, Leslie A. Kuhn:
Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes. 511-528 - Francesco Manzoni, Ulf Ryde:
Assessing the stability of free-energy perturbation calculations by performing variations in the method. 529-536 - Peter A. Hunt, Matthew D. Segall, Jonathan D. Tyzack:
WhichP450: a multi-class categorical model to predict the major metabolising CYP450 isoform for a compound. 537-546 - Jian Gao, Li Liang, Qingqing Chen, Ling Zhang, Tonghui Huang:
Insight into the molecular mechanism of yeast acetyl-coenzyme A carboxylase mutants F510I, N485G, I69E, E477R, and K73R resistant to soraphen A. 547-557 - Shubhandra Tripathi, Gaurava Srivastava, Aastha Singh, A. P. Prakasham, Arvind S. Negi, Ashok Sharma:
Insight into microtubule destabilization mechanism of 3, 4, 5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis. 559-572 - Xin Zhang, Jason B. Cross, Jan Romero, Alexander Heifetz, Eric Humphries, Katie Hall, Yuchuan Wu, Sabrina Stucka, Jing Zhang, Haoqun Chandonnet, Blaise Lippa, M. Dominic Ryan, J. Christian Baber:
In-silico guided discovery of novel CCR9 antagonists. 573-582
Volume 32, Number 5, May 2018
- Sankalp Jain, Eleni Kotsampasakou, Gerhard F. Ecker:
Comparing the performance of meta-classifiers - a case study on selected imbalanced data sets relevant for prediction of liver toxicity. 583-590 - Luan Carvalho Martins, Pedro Henrique Monteiro Torres, Renata Barbosa de Oliveira, Pedro Geraldo Pascutti, Elio A. Cino, Rafaela Salgado Ferreira:
Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations. 591-605 - Érica C. M. Nascimento, Mónica Oliva, Juan Andrés:
Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase. 607-622 - Francesca Cardamone, Mattia Falconi, Alessandro Desideri:
Molecular dynamics characterization of the SAMHD1 Aicardi-Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization. 623-632 - Lu Lu, Hua Yu:
DR2DI: a powerful computational tool for predicting novel drug-disease associations. 633-642 - Songling Ma, Jiwon Choi, Xuemei Jin, Hyun-Yi Kim, Jihye Yun, Weontae Lee, Kang-Yell Choi, Kyoung Tai No:
Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches. 643-655
Volume 32, Number 6, June 2018
- Mazen Y. Hamed:
Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations. 657-669 - Timothy Cholko, Wei Chen, Zhiye Tang, Chia-en A. Chang:
A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery. 671-685 - Thandokuhle Ntombela, Zeynab Fakhar, Collins U. Ibeji, Thavendran Govender, Glenn E. M. Maguire, Gyanu Lamichhane, Hendrik G. Kruger, Bahareh Honarparvar:
Molecular insight on the non-covalent interactions between carbapenems and l, d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study. 687-701 - Erick Martins Ratamero, Dom Bellini, Christopher G. Dowson, Rudolf A. Römer:
Touching proteins with virtual bare hands - Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware. 703-709 - Sofja Tshepelevitsh, Kertu Hernits, Ivo Leito:
Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS. 711-722
Volume 32, Number 7, July 2018
- Dimitris K. Agrafiotis, M. Katharine Holloway, Scott A. Johnson, Charles H. Reynolds, Terry R. Stouch, Alexander Tropsha, Chris L. Waller:
Chemistry, information and Frank: a tribute to Frank Brown. 723-729 - Ann E. Cleves, Ajay N. Jain:
Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. 731-757 - Tomoyuki Miyao, Jürgen Bajorath:
Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching. 759-767 - Saveliy Belkin, Petras J. Kundrotas, Ilya A. Vakser:
Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. 769-779 - Marcela Vettorazzi, Cintia Menéndez, Lucas Gutierrez, Sebastian A. Andujar, Gustavo Appignanesi, Ricardo D. Enriz:
Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis. 781-791 - Shibaji Ghosh, Kalyanashis Jana, Bishwajit Ganguly:
Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies. 793-807
Volume 32, Number 8, August 2018
- Yvonne C. Martin:
How medicinal chemists learned about log P. 809-819 - Hemavathy Nagarajan, Umashankar Vetrivel:
Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: an in silico approach. 821-840 - Matthew Habgood:
Conformational ensemble comparison for small molecules in drug discovery. 841-852 - Minh Khoa Nguyen, Léonard Jaillet, Stéphane Redon:
Generating conformational transition paths with low potential-energy barriers for proteins. 853-867 - Mauricio Carrillo-Tripp, Leonardo Alvarez-Rivera, Omar Israel Lara-Ramírez, Francisco Javier Becerra-Toledo, Adan Vega-Ramírez, Emmanuel Quijas-Valades, Eduardo González-Zavala, Julio Cesar González-Vázquez, Javier García-Vieyra, Nelly Beatriz Santoyo-Rivera, Sergio Víctor Chapa Vergara, Amilcar Meneses Viveros:
HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data. 869-876
Volume 32, Number 9, September 2018
- Michael Zhenin, Malkeet Singh Bahia, Gilles Marcou, Alexandre Varnek, Hanoch Senderowitz, Dragos Horvath:
Rescoring of docking poses under Occam's Razor: are there simpler solutions? 877-888 - D. Sam Paul, N. Gautham:
Protein-small molecule docking with receptor flexibility in iMOLSDOCK. 889-900 - Yaping Li, Yinglan Pu, Hui Liu, Li Zhang, Xingyong Liu, Yan Li, Zhili Zuo:
Discovery of novel wee1 inhibitors via structure-based virtual screening and biological evaluation. 901-915 - Jie Chen, Xiao Lin, Kyoung Jin Park, Kang Ro Lee, Hyun-Ju Park:
Identification of protoberberine alkaloids as novel histone methyltransferase G9a inhibitors by structure-based virtual screening. 917-928 - Piya Patra, Mahua Ghosh, Raja Banerjee, Jaydeb Chakrabarti:
Quantum chemical studies on anion specificity of CαNN motif in functional proteins. 929-936
Volume 32, Number 10, October 2018
- Andrea Rizzi, Steven Murkli, John N. McNeill, Wei Yao, Matthew R. Sullivan, Michael K. Gilson, Michael Chiu, Lyle Isaacs, Bruce C. Gibb, David L. Mobley, John D. Chodera:
Overview of the SAMPL6 host-guest binding affinity prediction challenge. 937-963 - Piero Procacci, Massimiliano Guarrasi, Guido Guarnieri:
SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach. 965-982 - Phillip S. Hudson, Kyungreem Han, H. Lee Woodcock III, Bernard R. Brooks:
Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. 983-999 - Tom Dixon, Samuel D. Lotz, Alex Dickson:
Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge. 1001-1012 - Lin Frank Song, Nupur Bansal, Zheng Zheng, Kenneth M. Merz Jr.:
Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge. 1013-1026 - Octav Caldararu, Martin A. Olsson, Majda Misini Ignjatovic, Meiting Wang, Ulf Ryde:
Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. 1027-1046 - Michail Papadourakis, Stefano Bosisio, Julien Michel:
Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge. 1047-1058 - Kyungreem Han, Phillip S. Hudson, Michael R. Jones, Naohiro Nishikawa, Florentina Tofoleanu, Bernard R. Brooks:
Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. 1059-1073 - Naohiro Nishikawa, Kyungreem Han, Xiongwu Wu, Florentina Tofoleanu, Bernard R. Brooks:
Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. 1075-1086 - Marie L. Laury, Zhi Wang, Aaron S. Gordon, Jay W. Ponder:
Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field. 1087-1095 - Yigitcan Eken, Prajay Patel, Thomas Díaz, Michael R. Jones, Angela K. Wilson:
SAMPL6 host-guest challenge: binding free energies via a multistep approach. 1097-1115 - Mehtap Isik, Dorothy Levorse, Ariën S. Rustenburg, Ikenna E. Ndukwe, Heather Wang, Xiao Wang, Mikhail Y. Reibarkh, Gary E. Martin, Alexey A. Makarov, David L. Mobley, Timothy Rhodes, John D. Chodera:
pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. 1117-1138 - Philipp Pracht, Rainer Wilcken, Anikó Udvarhelyi, Stephane Rodde, Stefan Grimme:
High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge. 1139-1149 - Nicolas Tielker, Lukas Eberlein, Stefan Güssregen, Stefan M. Kast:
The SAMPL6 challenge on predicting aqueous pK a values from EC-RISM theory. 1151-1163 - Caitlin C. Bannan, David L. Mobley, A. Geoffrey Skillman:
SAMPL6 challenge results from a predictions based on a general Gaussian process model. 1165-117 - Qiao Zeng, Michael R. Jones, Bernard R. Brooks:
Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge. 1179-1189 - Samarjeet Prasad, Jing Huang, Qiao Zeng, Bernard R. Brooks:
An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. 1191-1201 - Edithe Selwa, Ian M. Kenney, Oliver Beckstein, Bogdan I. Iorga:
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies. 1203-1216
Volume 32, Number 11, November 2018
- Youlin Xue, Qiaoshi Zhang, Yuna Sun, Xiaohong Zhou, Ian P. Hurley, Gary W. Jones, Youtao Song:
Using steered molecular dynamics to study the interaction between ADP and the nucleotide-binding domain of yeast Hsp70 protein Ssa1. 1217-1227 - Noriyuki Yamaotsu, Shuichi Hirono:
In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery. 1229-1245 - Irena Majerz:
Weak interactions in furan dimers. 1247-1258 - Paulo Siani, Himanshu Khandelia, M. Orsi, Luis Gustavo Dias:
Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. 1259-1271 - Gonzalo Cerruela García, Nicolás García-Pedrajas:
Boosted feature selectors: a case study on prediction P-gp inhibitors and substrates. 1273-1294 - Laurence Leherte, Axel Petit, Denis Jacquemin, Daniel P. Vercauteren, Adèle D. Laurent:
Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods. 1295-1313
Volume 32, Number 12, December 2018
- Julio Caballero, Alejandro Morales-Bayuelo, Carlos Navarro-Retamal:
Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. 1315-1336 - Enrico Margiotta, Giuseppe Deganutti, Stefano Moro:
Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench. 1337-1346 - E. Srinivasan, R. Rajasekaran:
Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein. 1347-1361 - Wen Hu, Liu Qin, Menglong Li, Xuemei Pu, Yanzhi Guo:
Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction. 1363-1373 - Stefan A. P. Lenz, Stacey D. Wetmore:
Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations. 1375-1388
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