Search results for "ligand"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
116	Maria I. Zavodszky, Andrew W. Stumpff-Kane, David J. Lee, Michael Feig	Scoring confidence index: statistical evaluation of ligand binding mode predictions.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Binding orientation, Correlation-based score, Energy landscape, Scoring function, Protein-ligand docking
104	William Novak, Hongming Wang, Goran Krilov	Role of protein flexibility in the design of Bcl-XL targeting agents: insight from molecular dynamics.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Protein flexibility, Protein-protein interfaces, Bcl-XL, Ligand-protein interactions, ABT-737, Molecular dynamics
103	Hooman Shadnia, James S. Wright, James M. Anderson	Interaction force diagrams: new insight into ligand-receptor binding.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Force vectors, Interaction Force Fingerprints, IFFP, Ligand-receptor, Estrogen receptor, Selectivity
93	Hiroshi Kobayashi, Ryuzo Azuma, Akihiko Konagaya	Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation.	AINA Workshops (1)	2007	DBLP DOI BibTeX RDF
90	Kimberly A. Reynolds, Vsevolod Katritch, Ruben Abagyan	Identifying conformational changes of the beta2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	?2 Adrenoceptor, Agonist, Virtual ligand screening, GPCR, MMFF, Homology model, G-protein coupled receptor
80	Prasad Gunasekaran, Scott Grandison, Kevin Cowtan, Lora Mak, David M. Lawson, Richard J. Morris	Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors.	PRIB	2009	DBLP DOI BibTeX RDF	electron density, protein crystallography, 3D Zernike moments, pattern recognition, structural bioinformatics
80	Joanna Lipinski-Kruszka, Rahul Singh	Integrative Geometric-Hashing Approaches to Binding Site Modeling and Ligand-Protein Interaction Prediction.	ISVC (1)	2007	DBLP DOI BibTeX RDF
80	Mehrdad Ghaemi, Nasrollah Rezaei-Ghaleh, Mohammad-Nabi Sarbolouki	Directed Ligand Passage over the Surface of Diffusion-Controlled Enzymes: A Cellular Automata Model.	ACRI	2004	DBLP DOI BibTeX RDF
76	Oliver Korb, Thomas Stützle, Thomas E. Exner	An ant colony optimization approach to flexible protein-ligand docking.	Swarm Intell.	2007	DBLP DOI BibTeX RDF	Cross-docking, Ant colony optimization, Virtual screening, Protein-ligand docking
76	Bekir Ergüner, Özgün Erdogan, Osman Ugur Sezerman	Prediction and Classification for GPCR Sequences Based on Ligand Specific Features.	ISCIS	2006	DBLP DOI BibTeX RDF	G-Protein Coupled Receptors (GPCRs), ligand specificity, GPCR sequence
66	Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. Das 0001	A Computationally Fast and Parametric Model to Estimate Protein-Ligand Docking Time for Stochastic Event Based Simulation.	Trans. Comp. Sys. Biology	2007	DBLP DOI BibTeX RDF
63	Wensheng Shen, Changjiang Zhang, Jun Zhang 0001	Multiscale simulation of ligand-receptor binding and dissociation in circulation.	ACM Southeast Regional Conference	2007	DBLP DOI BibTeX RDF	ligand-receptor interaction, multiscale modeling, nonlinear differential equation
54	Oliver Korb, Thomas Stützle, Thomas E. Exner	PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design.	ANTS Workshop	2006	DBLP DOI BibTeX RDF
54	Jinn-Moon Yang	An Evolutionary Approach for Molecular Docking.	GECCO	2003	DBLP DOI BibTeX RDF
53	Bo-Fu Liu, Hung-Ming Chen, Hui-Ling Huang, Shiow-Fen Hwang, Shinn-Ying Ho	Flexible protein-ligand docking using particle swarm optimization.	Congress on Evolutionary Computation	2005	DBLP DOI BibTeX RDF
53	Darby Tien-Hao Chang, Chien-Yu Chen 0001, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang	An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures.	BIBE	2004	DBLP DOI BibTeX RDF	protein structural analysis, protein tertiary structure, kernel density estimation
53	Vladimir V. Krepets, Natalya V. Belkina	Prediction of Binding Affinities for Protein-ligand Complexes with Neural Network Models.	Discovery Science	2000	DBLP DOI BibTeX RDF
50	Ignasi Belda, Xavier Llorà, Ernest Giralt	Evolutionary algorithms and de novo peptide design.	Soft Comput.	2006	DBLP DOI BibTeX RDF	Ligand design, Peptide design, Genetic algorithms, Evolutionary algorithms, Surface patch
50	Ryan H. Lilien, Brian W. Stevens, Amy C. Anderson, Bruce Randall Donald	A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme.	RECOMB	2004	DBLP DOI BibTeX RDF	enzyme design, fluorescence binding assay, molecular ensemble, non-ribosomal peptide synthetase, protein flexibility, protein-ligand binding, protein design
49	Abiola Oduguwa, Ashutosh Tiwari, S. Fiorentino, Rajkumar Roy	Multi-objective optimisation of the protein-ligand docking problem in drug discovery.	GECCO	2006	DBLP DOI BibTeX RDF	evolutionary computing, drug discovery, multi-objective optimisation, protein-ligand docking
40	Juan Cortés, Leonard Jaillet, Thierry Siméon	Molecular Disassembly With Rrt-Like Algorithms.	ICRA	2007	DBLP DOI BibTeX RDF
40	Yuval Inbar, Dina Schneidman-Duhovny, Oranit Dror, Ruth Nussinov, Haim J. Wolfson	Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules.	RECOMB	2007	DBLP DOI BibTeX RDF	Computer-Aided Drug Design (CADD), Rational Drug Discovery, 3D Molecular Similarity, 3D Molecular Superposition
40	Ruihai Cui, Jingping Zhang	Energy Partitioning Analysis of the Chemical Bonds in mer -Mq3 (M = AlIII, GaIII, InIII, TlIII).	International Conference on Computational Science (2)	2007	DBLP DOI BibTeX RDF	energy partitioning analysis, Mq3, FMO distribution fashion
40	Ashwin Srinivasan 0001, David Page, Rui Camacho, Ross D. King	Quantitative pharmacophore models with inductive logic programming.	Mach. Learn.	2006	DBLP DOI BibTeX RDF	Pharmacophore models, ILP, Statistical relational learning
40	Mikael Peräkylä	Molecular Dynamics Simulation Studies on the Modulation of Vitamin D Receptor Activity by Agonists and Antagonists.	PARA	2006	DBLP DOI BibTeX RDF
40	Andrei Oliveira da Silva, Osmar Norberto de Souza	A framework for result handling in bioinformatics: an application to computer assisted drug design.	SAC	2005	DBLP DOI BibTeX RDF	computer assisted drug design, frameworks, bioinformatics, molecular docking, high-throughput computing
40	Subhayu Basu, David K. Karig, Ron Weiss	Engineering signal processing in cells: Towards molecular concentration band detection.	Nat. Comput.	2003	DBLP DOI BibTeX RDF	cell-cell communications, genetic signal processing, synthetic gene networks, cellular computation
40	Subhayu Basu, David K. Karig, Ron Weiss	Engineering Signal Processing in Cells: Towards Molecular Concentration Band Detection.	DNA	2002	DBLP DOI BibTeX RDF
39	Ales Krenek, Martin Petrek, Jan Kmunícek, Jiri Filipovic, Zdenek Sustr, Frantisek Dvorák, Jirí Sitera, Jiri Wiesner, Ludek Matyska	Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services.	PDP	2008	DBLP DOI BibTeX RDF
39	Rafael Ördög, Vince Grolmusz	Evaluating Genetic Algorithms in Protein-Ligand Docking.	ISBRA	2008	DBLP DOI BibTeX RDF
39	Karina S. Machado, Evelyn K. Schroeder, Duncan D. Ruiz, Ana Wink, Osmar Norberto de Souza	Extracting Information from Flexible Receptor-Flexible Ligand Docking Experiments.	BSB	2008	DBLP DOI BibTeX RDF	AutoDock, Data Mining, Molecular Docking, Molecular Dynamics Simulation, WEKA
39	Scooter Willis	Protein CorreLogo: an X3D representation of co-evolving pairs, tertiary structure, ligand binding pockets and protein-protein interactions in protein families.	Web3D	2007	DBLP DOI BibTeX RDF	Protein CorreLogo, mutual information, X3D
39	David Abramson 0001, Céline Amoreira, Kim K. Baldridge, Laura Berstis, Chris Kondric, Tom Peachey	A Flexible Grid Framework for Automatic Protein-Ligand Docking.	e-Science	2006	DBLP DOI BibTeX RDF
39	Burcu Bakir, Osman Ugur Sezerman	Functional Classification of G-Protein Coupled Receptors, Based on Their Specific Ligand Coupling Patterns.	EvoWorkshops	2006	DBLP DOI BibTeX RDF
39	Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. Das 0001, Simon Daefler	A Stochastic model to estimate the time taken for Protein-Ligand Docking.	CIBCB	2006	DBLP DOI BibTeX RDF
39	Yaohang Li, Michael Mascagni, Michael H. Peter	Grid-based Nonequilibrium Multiple-Time Scale Molecular Dynamics/Brownian Dynamics Simulations of Ligand-Receptor Interactions in Structured Protein Systems.	CCGRID	2003	DBLP DOI BibTeX RDF
39	Ruben Abagyan	Computational structural proteomics and virtual ligand screening.	RECOMB	2002	DBLP DOI BibTeX RDF
38	Caihua Wang, Juan Liu 0007, Fei Luo 0004, Zixing Deng, Qian-Nan Hu	Predicting target-ligand interactions using protein ligand-binding site and ligand substructures.	BMC Syst. Biol.	2015	DBLP DOI BibTeX RDF
38	Yousef Jamali, Tahereh Jamali, Mohammad R. Kaazempur Mofrad	An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility.	J. Comput. Phys.	2013	DBLP DOI BibTeX RDF
38	Violeta I. Pérez-Nueno, David W. Ritchie, Obdulia Rabal, Rosalia Pascual, José I. Borrell, Jordi Teixidó	Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand-Receptor Docking.	J. Chem. Inf. Model.	2008	DBLP DOI BibTeX RDF
38	Markus H. J. Seifert	ProPose: Steered Virtual Screening by Simultaneous Protein-Ligand Docking and Ligand-Ligand Alignment.	J. Chem. Inf. Model.	2005	DBLP DOI BibTeX RDF
38	Jae-Min Shin, Doo-Ho Cho	PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures.	Nucleic Acids Res.	2005	DBLP DOI BibTeX RDF
37	Pekka Tiikkainen, Antti Poso, Olli-P. Kallioniemi	Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Ligand-based virtual screening, NCI-60, Chemical similarity, Data fusion
37	Yan-Li Hu, Liang Bai, Weiming Zhang 0003, Weidong Xiao, Zhong Liu	An Adaptive Scheduling Algorithm for Molecule Docking Design on Grid.	GCC	2005	DBLP DOI BibTeX RDF	ligand, receptor, time-balancing, Grid, jobs scheduling, Molecular docking
36	Lincong Wang	The Geometric and Electrostatic Properties of Binding Cavities and Their Usage in Protein-Ligand Docking.	FCST	2010	DBLP DOI BibTeX RDF	electrostatic interaction, Scoring function, Protein-ligand docking
36	Chong-Min Kim, Chung In Won, Joonghyun Ryu, Jae-Kwan Kim 0001, Jong Bhak, Deok-Soo Kim	Protein-Ligand Docking Based on ss-shape.	ISVD	2009	DBLP DOI BibTeX RDF	ß-shape, pocket, Voronoi diagram, Protein-ligand docking
27	Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine	Rule-Based Modelling and Model Perturbation.	Trans. Comp. Sys. Biology	2009	DBLP DOI BibTeX RDF
27	Jacob Kongsted, Ulf Ryde	An improved method to predict the entropy term with the MM/PBSA approach.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	MM/PBSA, Avidin, Factor Xa, Cytochrome P450, Entropy
27	Haiyun Lu, Hao Li 0032, Shamima Banu Bte Sm Rashid, Wee Kheng Leow, Yih-Cherng Liou	Knowledge-Guided Docking of WW Domain Proteins and Flexible Ligands.	PRIB	2009	DBLP DOI BibTeX RDF
27	Roberto Andreani, José Mario Martínez, Leandro Martínez, Flávio S. Yano	Continuous optimization methods for structure alignments.	Math. Program.	2008	DBLP DOI BibTeX RDF	Protein alignment, Order-value optimization, Continuous optimization, Gauss-Newton method, Structural alignment
27	Bruno Daunay, Alain Micaelli, Stephane Régnier	6 DOF haptic feedback for molecular docking using wave variables.	ICRA	2007	DBLP DOI BibTeX RDF
27	Gennady Verkhivker	Computational Proteomics of Biomolecular Interactions in Sequence and Structure Space of the Tyrosine Kinome: Evolutionary Constraints and Protein Conformational Selection Determine Binding Signatures of Cancer Drugs.	WILF	2007	DBLP DOI BibTeX RDF
27	Petter Bivall Persson, Matthew D. Cooper, Lena A. E. Tibell, Shaaron Ainsworth, Anders Ynnerman, Bengt-Harald Jonsson	Designing and Evaluating a Haptic System for Biomolecular Education.	VR	2007	DBLP DOI BibTeX RDF
27	Anthonin Reilhac, Alan C. Evans, Gérard Gimenez, Nicolas Costes 0001	Creation and Application of a Simulated Database of Dynamic 18MPPF PET Acquisitions Incorporating Inter-Individual Anatomical and Biological Variability.	IEEE Trans. Medical Imaging	2006	DBLP DOI BibTeX RDF
27	Ignasi Belda, Xavier Llorà, Marc Martinell, Teresa Tarragó, Ernest Giralt	Computer-Aided Peptide Evolution for Virtual Drug Design.	GECCO (1)	2004	DBLP DOI BibTeX RDF
27	David P. Enot, Ross D. King	Application of Inductive Logic Programming to Structure-Based Drug Design.	PKDD	2003	DBLP DOI BibTeX RDF
27	Stephen H. Muggleton, Alireza Tamaddoni-Nezhad, Hiroaki Watanabe	Induction of Enzyme Classes from Biological Databases.	ILP	2003	DBLP DOI BibTeX RDF
27	Ehud Shapiro	Invited Lecture - Molecule as Computation: Towards an Abstraction of Biomolecular Systems.	WABI	2002	DBLP DOI BibTeX RDF
26	Giovanni Cincilla, David Vidal, Miquel Pons	An improved scoring function for suboptimal polar ligand complexes.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Solvation, Drug design, Virtual screening, Docking, Scoring function
26	Ling Kang, Honglin Li, Hualiang Jiang, Xicheng Wang	An improved adaptive genetic algorithm for protein-ligand docking.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	Genetic algorithms, Self-adaptation, Optimization design, Information entropy, Molecular docking, Penalty function
26	Jorge Tavares, Alexandru-Adrian Tantar, Nouredine Melab, El-Ghazali Talbi	The Influence of Mutation on Protein-Ligand Docking Optimization: A Locality Analysis.	PPSN	2008	DBLP DOI BibTeX RDF
26	Sunil Kumar, Rajni Garg, Srinivas R. Alla, Xiaoyu Zhang, Vivek K. Jalahalli	3D-Shape analysis of the HIV-1 protease ligand binding site.	CIBCB	2008	DBLP DOI BibTeX RDF
26	Paul E. Anderson 0001, Douglas W. Raiford, Deacon J. Sweeney, Travis E. Doom, Michael L. Raymer	Stochastic Model of Protease-Ligand Reactions.	BIBE	2005	DBLP DOI BibTeX RDF
26	Michela Taufer, Michael F. Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III	Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics.	IPDPS	2004	DBLP DOI BibTeX RDF	Force field based methods, docking accuracy, desktop grid computing
25	Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie, Ren Kong, Shan Chang	CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction.	BMC Bioinform.	2023	DBLP DOI BibTeX RDF
25	Yuyu Feng 0002, Keqiong Zhang, Qilong Wu 0001, Sheng-You Huang	NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Joanna M. Zarnecka, Iva Lukac, Stephen J. Messham, Alhusein Hussin, Francesco Coppola, Steven J. Enoch, Alexander G. Dossetter, Edward J. Griffen, Andrew G. Leach	Mapping Ligand-Shape Space for Protein-Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Hugo Guterres, Sang-Jun Park, Yiwei Cao, Wonpil Im	CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
25	Takeshi Ashida, Takeshi Kikuchi	A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase-ligand and FKBP-ligand systems.	J. Comput. Aided Mol. Des.	2020	DBLP DOI BibTeX RDF
25	Dinesh Kumar Sriramulu, Sun-Gu Lee	Combinatorial Effect of Ligand and Ligand-Binding Site Hydrophobicities on Binding Affinity.	J. Chem. Inf. Model.	2020	DBLP DOI BibTeX RDF
25	Fergus Boyles, Charlotte M. Deane, Garrett M. Morris	Learning from the ligand: using ligand-based features to improve binding affinity prediction.	Bioinform.	2020	DBLP DOI BibTeX RDF
25	Melanie Schneider, Jean-Luc Pons, William Bourguet, Gilles Labesse	Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity.	Bioinform.	2020	DBLP DOI BibTeX RDF
25	Sebastian Raschka, Benjamin Kaufman	Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition.	CoRR	2020	DBLP BibTeX RDF
25	Meng Chi Ao, Shirley W. I. Siu	Evaluating Variants of Firefly Algorithm for Ligand Pose Prediction in Protein-ligand Docking Program.	ICBBT	2020	DBLP DOI BibTeX RDF
25	Jinsol Yang, Minkyung Baek, Chaok Seok	GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility.	J. Comput. Chem.	2019	DBLP DOI BibTeX RDF
25	Saad Raza, Kara E. Ranaghan, Marc van der Kamp, Christopher J. Woods, Adrian J. Mulholland, Syed Sikander Azam	Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site.	J. Comput. Aided Mol. Des.	2019	DBLP DOI BibTeX RDF
25	Vincent D. Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu 0002, Wenjuan Jiang, Alexander D. MacKerell Jr.	Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization.	J. Chem. Inf. Model.	2019	DBLP DOI BibTeX RDF
25	Anmona Shabnam Pranti, Daniel Loof, Sebastian Kunz, Volkmar Zielasek, Marcus Bäumer, Walter Lang	Ligand-Linked Nanoparticles-Based Hydrogen Gas Sensor with Excellent Homogeneous Temperature Field and a Comparative Stability Evaluation of Different Ligand-Linked Catalysts.	Sensors	2019	DBLP DOI BibTeX RDF
25	Zhirui Liao, Ronghui You, Xiaodi Huang, Xiaojun Yao, Tao Huang, Shanfeng Zhu	DeepDock: Enhancing Ligand-protein Interaction Prediction by a Combination of Ligand and Structure Information.	BIBM	2019	DBLP DOI BibTeX RDF
25	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.	J. Comput. Aided Mol. Des.	2018	DBLP DOI BibTeX RDF
25	Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov	Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.	J. Comput. Aided Mol. Des.	2018	DBLP DOI BibTeX RDF
25	Panagiotis Lagarias, Eleni Vrontaki, George Lambrinidis, Dimitrios Stamatis, Marino Convertino, Gabriella Ortore, Thomas M. Mavromoustakos, Karl Norbert Klotz, Antonios Kolocouris	Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode.	J. Chem. Inf. Model.	2018	DBLP DOI BibTeX RDF
25	Qi Wu 0016, Zhenling Peng, Yang Zhang 0040, Jianyi Yang	COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking.	Nucleic Acids Res.	2018	DBLP DOI BibTeX RDF
25	Peyton Greenside, Maureen Hillenmeyer, Anshul Kundaje	Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures.	PSB	2018	DBLP BibTeX RDF
25	Charles H. Reynolds, Ryan C. Reynolds	Group Additivity in Ligand Binding Affinity: An Alternative Approach to Ligand Efficiency.	J. Chem. Inf. Model.	2017	DBLP DOI BibTeX RDF
25	Yuedong Yang, Jian Zhan, Yaoqi Zhou	SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.	J. Comput. Chem.	2016	DBLP DOI BibTeX RDF
25	Sheng-You Huang, Min Li 0007, Jianxin Wang 0001, Yi Pan 0001	HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches.	J. Chem. Inf. Model.	2016	DBLP DOI BibTeX RDF
25	Pradeep Anand Ravindranath, Michel F. Sanner	AutoSite: an automated approach for pseudo-ligands prediction - from ligand-binding sites identification to predicting key ligand atoms.	Bioinform.	2016	DBLP DOI BibTeX RDF
25	Yu Du, Tieliu Shi	Ligand cluster-based protein network and ePlatton, a multi-target ligand finder.	J. Cheminformatics	2016	DBLP DOI BibTeX RDF
25	Francesca Spyrakis, Paolo Benedetti, Sergio Decherchi, Walter Rocchia, Andrea Cavalli, Stefano Alcaro, Francesco Ortuso, Massimo Baroni, Gabriele Cruciani	A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.	J. Chem. Inf. Model.	2015	DBLP DOI BibTeX RDF
25	Qingliang Shen, Hong Tian, Daoqi Tang, Wenbing Yao, Xiangdong Gao	Ligand-K* Sequence Elimination: A NovelAlgorithm for Ensemble-Based Redesignof Receptor-Ligand Binding.	IEEE ACM Trans. Comput. Biol. Bioinform.	2014	DBLP DOI BibTeX RDF
25	Paraskevi Gkeka, Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia	Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion.	PLoS Comput. Biol.	2014	DBLP DOI BibTeX RDF
25	Marcus Malo, Ronnie Persson, Peder Svensson, Kristina Luthman, Lars Brive	Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor.	J. Comput. Aided Mol. Des.	2013	DBLP DOI BibTeX RDF
25	Shana L. Posy, Brian L. Claus, Matt E. Pokross, Stephen R. Johnson	3D Matched Pairs: Integrating Ligand- and Structure-Based Knowledge for Ligand Design and Receptor Annotation.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
25	Akira Shiraishi, Satoshi Niijima, J. B. Brown, Masahiko Nakatsui, Yasushi Okuno	Chemical Genomics Approach for GPCR-Ligand Interaction Prediction and Extraction of Ligand Binding Determinants.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
25	Vladimir I. Chupakhin, Gilles Marcou, Igor I. Baskin, Alexandre Varnek, Didier Rognan	Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
25	Zhong-Ru Xie, Chuan-Kun Liu, Fang-Chih Hsiao, Adam Yao, Ming-Jing Hwang	LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites.	Nucleic Acids Res.	2013	DBLP DOI BibTeX RDF
25	Fan Jin, Chen Yu, Luhua Lai, Zhirong Liu	Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins.	PLoS Comput. Biol.	2013	DBLP DOI BibTeX RDF
25	Ying-Ting Lin	A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.	J. Cheminformatics	2013	DBLP DOI BibTeX RDF
25	Pratyusha Rakshit, Amit Konar, Archana Chowdhury, Eunjin Kim, Atulya K. Nagar	Muti-objective evolutionary approach of ligand design for protein-ligand docking problem.	IEEE Congress on Evolutionary Computation	2013	DBLP DOI BibTeX RDF