Search results for "binding"

Hits ?▲	Authors	Title	Venue	Year	Link
9	Suvankar Ghosh, Sunanda Chatterjee, Priyadarshi Satpati	Effect of Spacer Length Modification of the Cationic Side Chain on the Energetics of Antimicrobial Peptide Binding to Membrane-Mimetic Bilayers.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Dahlia R. Weiss, Andrea Bortolato, Yongnian Sun, Xianmei Cai, Chon Lai, Sixuan Guo, Lihong Shi, Veerabahu Shanmugasundaram	On Ternary Complex Stability in Protein Degradation: In Silico Molecular Glue Binding Affinity Calculations.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Zheng Zhao, Niraja Bohidar, Philip E. Bourne	Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Mateusz K. Bieniek, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney	TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Song Li, Chao Hu, Song Ke, Chenxing Yang, Jun Chen, Yi Xiong, Hao Liu, Liang Hong	LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Zhenhao Liu, Kuan Liang, Wenlang Liu, Tao Jiang, Rui Zhou, Mojie Duan, Zheng Zheng 0002	Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Farzad Molani, Simon Webb, Art E. Cho	Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Jun Hu 0010, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang	Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Luís Queirós-Reis, João R. Mesquita, Andrea Brancale, Marcella Bassetto	Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Nuno M. S. Almeida, Semiha Kevser Bali, Deepak James, Cong Wang, Angela K. Wilson	Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Raitis Bobrovs, Laura Drunka, Iveta Kanepe, Aigars Jirgensons, Amedeo Caflisch, Matteo Salvalaglio, Kristaps Jaudzems	Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Hugo Guterres, Wonpil Im	CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Cristina González Fernández, Christoph Öhlknecht, Matthias Diem, Yerko Escalona, Eugenio Bringas, Gabriel Moncalián, Chris Oostenbrink, Inmaculada Ortiz	Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon: An In Silico Study through MD Simulations.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Francesc Sabanés Zariquiey, Adrià Pérez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis	Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Marcelo Depólo Polêto, Justin A. Lemkul	Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Jack B. Greisman, Lindsay Willmore, Christine Y. Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter M. Nisonoff, Paul Maragakis, David E. Shaw	Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Jiaqi Liu, Jian Wan 0004, Yanliang Ren, Xubo Shao, Xin Xu 0004, Li Rao 0001	DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein-Ligand Binding Affinity Prediction.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Bin Sun 0005, Te Liu, Manjie Zhang, Shuijie Li	Synergistic Binding of ATP and Nucleic Acids Necessitates UPF1's ATPase Functional Cycle.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Yong Xiao Yang, Jin Yan Huang, Pan Wang, Bao Ting Zhu	AREA-AFFINITY: A Web Server for Machine Learning-Based Prediction of Protein-Protein and Antibody-Protein Antigen Binding Affinities.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Jialin Bi, Junjie Wee, Xiang Liu, Cunquan Qu, Guanghui Wang 0002, Kelin Xia	Multiscale Topological Indices for the Quantitative Prediction of SARS CoV-2 Binding Affinity Change upon Mutations.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Efpraxia Tzortzini, Robin A. Corey, Antonios Kolocouris	Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Sudarshan Behera, Sundaram Balasubramanian	Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Claudia Llinas del Torrent, Iu Raïch, Angel Gonzalez, Nil Casajuana-Martin, Jaume Lillo, Joan Biel Rebassa, Carlos Ferreiro-Vera, Verónica Sánchez de Medina, Rafael Franco, Gemma Navarro, Leonardo Pardo	The Leu/Val6.51 Side Chain of Cannabinoid Receptors Regulates the Binding Mode of the Alkyl Chain of Δ9-Tetrahydrocannabinol.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Anupam Anand Ojha, Ambuj Srivastava, Lane W. Votapka, Rommie E. Amaro	Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	M. Andrés Velasco-Saavedra, Efrén Mar-Antonio, Rodrigo Aguayo-Ortiz	Molecular Insights into the Covalent Binding of Zoxamide to the β-Tubulin of Botrytis cinerea.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Ran Liu, Xiang Liu, Jie Wu	Persistent Path-Spectral (PPS) Based Machine Learning for Protein-Ligand Binding Affinity Prediction.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Madelyn Smith, Pengfei Li 0003	Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Lijun Lang, Antonio Frontera, Alberto Perez, Antonio Bauzá	Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Abhik Ghosh Moulick, Jaydeb Chakrabarti	Fluctuation-Dominated Ligand Binding in Molten Globule Protein.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Lucas G. Viviani, Daria B. Kokh, Rebecca C. Wade, Antonia T. do Amaral	Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Sergei A. Evteev, Alexey V. Ereshchenko, Yan A. Ivanenkov	SiteRadar: Utilizing Graph Machine Learning for Precise Mapping of Protein-Ligand-Binding Sites.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai	Achieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Gregory W. Kyro, Rafael I. Brent, Victor S. Batista	HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Pabitra Narayan Samanta, Devashis Majumdar, Jerzy Leszczynski	Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Darren J. Hsu, Russell B. Davidson, Ada Sedova, Jens Glaser	tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Diego Enry Barreto Gomes, Katia Galentino, Marion Sisquellas, Luca Monari, Cédric Bouysset, Marco Cecchini	ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Mohammad Mehdi Ghahremanpour, Anastasia Saar, Julian Tirado-Rives, William L. Jorgensen	Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Xiaokun Hong, Kaiyuan Song, Mueed Ur Rahman, Ting Wei, Yan Zhang, Lin-Tai Da, Hai-Feng Chen	Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Keshavan Seshadri, Marimuthu Krishnan	Molecular Dynamics and Machine Learning Study of Adrenaline Dynamics in the Binding Pocket of GPCR.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Vid Ravnik, Marko Jukic, Urban Bren	Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Filipp Gusev, Evgeny Gutkin, Maria G. Kurnikova, Olexandr Isayev	Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Almotasem Belah Alhamwi, Canan Atilgan, Özge Sensoy	Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW-Penicillin-Binding Protein 3 Complex of Haemophilus influenzae.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Sutong Xiang, Zhe Wang, Rongfan Tang, Lingling Wang, Qinghua Wang, Yang Yu, Qirui Deng, Tingjun Hou, Haiping Hao, Huiyong Sun	Exhaustively Exploring the Prevalent Interaction Pathways of Ligands Targeting the Ligand-Binding Pocket of Farnesoid X Receptor via Combined Enhanced Sampling.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill	MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Alessandro Nicoli, Franziska Haag, Patrick Marcinek, Ruiming He, Johanna Kreißl, Jörg Stein, Alessandro Marchetto 0002, Andreas Dunkel, Thomas Hofmann, Dietmar Krautwurst, Antonella Di Pizio	Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Yishui Li, Runduo Liu, Jie Liu 0002, Haibin Luo, Chengkun Wu, Zhe Li	An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Martin Ljubic, Eva Prasnikar, Andrej Perdih, Jure Borisek	All-Atom Simulations Reveal the Intricacies of Signal Transduction upon Binding of the HLA-E Ligand to the Transmembrane Inhibitory CD94/NKG2A Receptor.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Niu Zhang, Zhicheng Zuo	Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera	Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Daniel R. Bryan, John L. Kulp Jr., Manoj K. Mahapatra, Richard L. Bryan, Usha Viswanathan, Micah N. Carlisle, Surim Kim, William D. Schutte, Kevaughn V. Clarke, Tony T. Doan, John L. Kulp III	BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Yuko Tsuchiya, Tomoki Yonezawa, Yu Yamamori, Hiroko Inoura, Masanori Osawa, Kazuyoshi Ikeda, Kentaro Tomii	PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Vincenzo Maria D'amore, Greta Donati, Elena Lenci, Beatrice Stefanie Ludwig, Susanne Kossatz, Monica Baiula, Andrea Trabocchi, Horst Kessler, Francesco Saverio Di Leva, Luciana Marinelli	Molecular View on the iRGD Peptide Binding Mechanism: Implications for Integrin Activity and Selectivity Profiles.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Anastasia Saar, Mohammad Mehdi Ghahremanpour, Julian Tirado-Rives, William L. Jorgensen	Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Rubina, Syed Tarique Moin	Attempting Well-Tempered Funnel Metadynamics Simulations for the Evaluation of the Binding Kinetics of Methionine Aminopeptidase-II Inhibitors.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Christopher Lockhart, Xingyu Luo, Audrey Olson, Bryan M. Delfing, Xavier E. Laracuente, Kenneth W. Foreman, Mikell Paige, Kylene Kehn-Hall, Dmitri K. Klimov	Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites?	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Garrett A. Stevenson, Dan Kirshner 0001, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam T. Zemla, Marisa W. Torres, Aidan Epstein, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Sergio Ernesto Wong, Jonathan E. Allen, Felice C. Lightstone	Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Steffen Wolf	Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Natasha Gupta Vergara, Megan Gatchel, Cameron F. Abrams	Entropic Overcompensation of the N501Y Mutation on SARS-CoV-2 S Binding to ACE2.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Katsuki Takebe, Mamoru Suzuki, Takao Kuwada-Kusunose, Satoko Shirai, Kaori Fukuzawa, Tomoko Takamiya, Narikazu Uzawa, Hiroshi Iijima	Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Runduo Liu, Wenchao Li, Yufen Yao, Yinuo Wu, Hai-Bin Luo, Zhe Li	Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9	Chris Zhang 0002, Mary Pitman, Anjali Dixit, Sumudu Leelananda, Henri Palacci, Meghan Lawler, Svetlana Belyanskaya, Lashadric Grady, Joe Franklin, Nicolas Tilmans, David L. Mobley	Building Block-Based Binding Predictions for DNA-Encoded Libraries.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
9		Towards a purely physics-based computational binding affinity estimation.	Nat. Comput. Sci.	2023	DBLP DOI BibTeX RDF
9	Vivek Govind Kumar, Adithya Polasa, Shilpi Agrawal, Thallapuranam K. Suresh Kumar, Mahmoud Moradi	Binding affinity estimation from restrained umbrella sampling simulations.	Nat. Comput. Sci.	2023	DBLP DOI BibTeX RDF
9		Efficient prediction of relative ligand binding affinity in drug discovery.	Nat. Comput. Sci.	2023	DBLP DOI BibTeX RDF
9	Xinchi Yu, Ellen Lau	The Binding Problem 2.0: Beyond Perceptual Features.	Cogn. Sci.	2023	DBLP DOI BibTeX RDF
9	Binjie Guo, Hanyu Zheng, Haohan Jiang, Xiaodan Li, Naiyu Guan, Yanming Zuo, Yicheng Zhang, Hengfu Yang, Xuhua Wang	Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Natalia A Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak	Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Yu Zhao 0009, Xiaona Su, Weitong Zhang, Sijie Mai, Zhimeng Xu, Chenchen Qin, Rongshan Yu, Bing He, Jianhua Yao 0001	SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Yidong Song, Qianmu Yuan, Huiying Zhao, Yuedong Yang	Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Manuel Tognon, Rosalba Giugno, Luca Pinello	A survey on algorithms to characterize transcription factor binding sites.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Yi-Gang Chen, Yang-Chi-Dung Lin, Yijun Luo, Xiao-Xuan Cai, Peng Qiu, Shi-Dong Cui, Zhe Wang, Hsi-Yuan Huang, Hsien-Da Huang	Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Zheng Ye, Shaohao Li, Xue Mi, Baoyi Shao, Zhu Dai, Bo Ding, Songwei Feng, Bo Sun, Yang Shen, Zhongdang Xiao	STMHCpan, an accurate Star-Transformer-based extensible framework for predicting MHC I allele binding peptides.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Ran Liu, Ye-Fan Hu, Jian-Dong Huang, Xiaodan Fan	A Bayesian approach to estimate MHC-peptide binding threshold.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Yuepeng Jiang, Miaozhe Huo, Shuai Cheng Li	TEINet: a deep learning framework for prediction of TCR-epitope binding specificity.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen	Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Hongjun Chen, Yekai Zhou, Yongjing Liu, Peijing Zhang, Ming Chen 0005	Network integration and protein structural binding analysis of neurodegeneration-related interactome.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Yanpeng Zhao, Jingjing Wang, Fubin Chang, Weikang Gong, Yang Liu, Chunhua Li	Identification of metal ion-binding sites in RNA structures using deep learning method.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Shukai Gu, Chao Shen, Jiahui Yu, Hong Zhao, Huanxiang Liu, Liwei Liu, Rong Sheng, Lei Xu 0035, Zhe Wang 0041, Tingjun Hou, Yu Kang 0002	Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Yutong Yu, Pengju Ding, Hongli Gao, Guozhu Liu, Fa Zhang, Bin Yu 0007	Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Jiaxian Yan, Zhaofeng Ye, Ziyi Yang, Chengqiang Lu, Shengyu Zhang, Qi Liu, Jiezhong Qiu	Multi-task bioassay pre-training for protein-ligand binding affinity prediction.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Pengju Ding, Yifei Wang, Xinyu Zhang, Xin Gao 0001, Guozhu Liu, Bin Yu 0007	DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Kaili Wang, Renyi Zhou, Yifan Wu, Min Li 0007	RLBind: a deep learning method to predict RNA-ligand binding sites.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Soumen Pal, Ajit Gupta, Rajender Parsad	PlDBPred: a novel computational model for discovery of DNA binding proteins in plants.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Lishen Zhang, Chengqian Lu, Min Zeng, Yaohang Li, Jianxin Wang 0001	CRMSS: predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Meng Wang, Lukasz A. Kurgan, Min Li 0007	A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Zhiqiang Hu, Wenfeng Liu, Chenbin Zhang, Jiawen Huang, Shaoting Zhang 0001, Huiqun Yu, Yi Xiong, Hao Liu, Song Ke, Liang Hong	SAM-DTA: a sequence-agnostic model for drug-target binding affinity prediction.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
9	Walter Arancio, Nicolina Sciaraffa, Claudia Coronnello	MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome.	Database J. Biol. Databases Curation	2023	DBLP DOI BibTeX RDF
9	Darius Linge, Marius Gedgaudas, Andrius Merkys, Vytautas Petrauskas, Antanas Vaitkus, Algirdas Grybauskas, Vaida Paketuryte, Asta Zubriene, Audrius Zaksauskas, Aurelija Mickeviciute, Joana Smirnoviene, Lina Baranauskiene, Edita Capkauskaite, Virginija Dudutiene, Ernestas Urniezius, Aleksandras Konovalovas, Egidijus Kazlauskas, Kirill Shubin, Helgi B. Schiöth, Wen-Yih Chen, John E. Ladbury, Saulius Grazulis, Daumantas Matulis	PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters.	Database J. Biol. Databases Curation	2023	DBLP DOI BibTeX RDF
9	Naoki Hiratani, Haim Sompolinsky	Optimal Quadratic Binding for Relational Reasoning in Vector Symbolic Neural Architectures.	Neural Comput.	2023	DBLP DOI BibTeX RDF
9	Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös 0002, Silvio C. E. Tosatto, Damiano Piovesan	CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Louis Philip Benoit Bouvrette, Xiaofeng Wang, Jonathan Boulais, Jian Kong, Easin Uddin Syed, Steven M. Blue, Lijun Zhan, Sara Olson, Rebecca Stanton, Xintao Wei, Brian Yee, Eric L. Van nostrand, Xiang-Dong Fu, Christopher B. Burge, Brenton R. Graveley, Gene W. Yeo, Eric Lécuyer	RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Sébastien Bourdon, Pauline Herviou, Leïla Dumas, Eliana Destefanis, Andrea Zen, Anne Cammas, Stefania Millevoi, Erik Dassi	QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Kai Liu, Xufeng Lu, Hang Shi, Xiaojun Xu, Ren Kong, Shan Chang	nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Daniel M. Tadros, Simon Eggenschwiler, Julien Racle, David Gfeller	The MHC Motif Atlas: a database of MHC binding specificities and ligands.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Yongbing Zhao	TFSyntax: a database of transcription factors binding syntax in mammalian genomes.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Jiho Sim, Sohee Kwon, Chaok Seok	HProteome-BSite: predicted binding sites and ligands in human 3D proteome.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	András Hatos, João M. C. Teixeira, Susana Barrera-Vilarmau, Attila Horvath, Silvio C. E. Tosatto, Michele Vendruscolo, Mónika Fuxreiter	FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins.	Nucleic Acids Res.	2023	DBLP DOI BibTeX RDF
9	Michael Zuzak, Yuntao Liu 0001, Ankur Srivastava 0001	Security-Aware Resource Binding to Enhance Logic Obfuscation.	IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.	2023	DBLP DOI BibTeX RDF
9	A. Mallika, J. Ahamed Thamimul Ansari	Binding number for coprime graph of groups.	AKCE Int. J. Graphs Comb.	2023	DBLP DOI BibTeX RDF
9	Yue Li, Fengyun Ren, Xin Xu, Qinghe Tong	Tight toughness, isolated toughness and binding number bounds for the path factors.	Int. J. Comput. Math. Comput. Syst. Theory	2023	DBLP DOI BibTeX RDF