Search results for "binding"

Hits ?▲	Authors	Title	Venue	Year	Link
9	Arash Mollahosseini, Shaghayegh Saadati, Amira Abdelrasoul	Effects of mussel-inspired co-deposition of 2-hydroxymethyl methacrylate and poly (2-methoxyethyl acrylate) on the hydrophilicity and binding tendency of common hemodialysis membranes: Molecular dynamics simulations and molecular docking studies.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
9	Yuqing Xiong, Juan Zeng, Fei Xia, Qiang Cui, Xianming Deng, Xin Xu 0004	Conformations and binding pockets of HRas and its guanine nucleotide exchange factors complexes in the guanosine triphosphate exchange process.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
9	Tymofii Yu. Nikolaienko, Oleksandr Gurbych, Maksym Druchok	Complex machine learning model needs complex testing: Examining predictability of molecular binding affinity by a graph neural network.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
9	Yingsheng Zhou, Justin M. Overhulse, Nathan J. Dupper, Yanchun Guo, Boris A. Kashemirov, Kaiyao Wei, Jérôme Govin, Carlo Petosa, Charles E. McKenna	Toward more potent imidazopyridine inhibitors of Candida albicans Bdf1: Modeling the role of structural waters in selective ligand binding.	J. Comput. Chem.	2022	DBLP DOI BibTeX RDF
9	Yuqian Pu, Jiawei Li, Jijun Tang, Fei Guo 0001	DeepFusionDTA: Drug-Target Binding Affinity Prediction With Information Fusion and Hybrid Deep-Learning Ensemble Model.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Fang Jing, Shaowu Zhang 0001, Shihua Zhang	Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan 0001, Yuedong Yang	To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Zhen Shen, Qinhu Zhang, Kyungsook Han, De-Shuang Huang	A Deep Learning Model for RNA-Protein Binding Preference Prediction Based on Hierarchical LSTM and Attention Network.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang 0001, Renyi Zhou, Min Li 0007	In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Zhaowei Wang 0005, Qiguo Dai, Jinmiao Song, Xiaodong Duan, Hongpeng Yang, Ziqi Yang	Predicting RBP Binding Sites of RNA With High-Order Encoding Features and CNN-BLSTM Hybrid Model.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Mohammad A. Rezaei, Yanjun Li 0005, Dapeng Wu 0001, Xiaolin Li 0001, Chenglong Li	Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Jingshu Bi, Yuanjie Zheng, Chongjing Wang, Yanhui Ding	An Attention Based Bidirectional LSTM Method to Predict the Binding of TCR and Epitope.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Qinhu Zhang, Yindong Zhang, Siguo Wang, Zhan-Heng Chen, Valeriya V. Gribova, Vladimir Fedorovich Filaretov, De-Shuang Huang	Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Lijun Quan, Xiaoyu Sun 0006, Jian Wu, Jie Mei, Liqun Huang, Ruji He, Liangpeng Nie, Yu Chen 0064, Qiang Lyu	Learning Useful Representations of DNA Sequences From ChIP-Seq Datasets for Exploring Transcription Factor Binding Specificities.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Jun Hu 0010, Yan-Song Bai, Lin-Lin Zheng, Ning-Xin Jia, Dong-Jun Yu, Gui-Jun Zhang	Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Nassima Aleb	A Mutual Attention Model for Drug Target Binding Affinity Prediction.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Ning Wang, Jun Zhang, Bin Liu 0014	IDRBP-PPCT: Identifying Nucleic Acid-Binding Proteins Based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Zhonghao Liu, Jing Jin, Yuxin Cui, Zheng Xiong, Alireza Nasiri, Yong Zhao 0014, Jianjun Hu	DeepSeqPanII: An Interpretable Recurrent Neural Network Model With Attention Mechanism for Peptide-HLA Class II Binding Prediction.	IEEE ACM Trans. Comput. Biol. Bioinform.	2022	DBLP DOI BibTeX RDF
9	Andreas Tosstorff, Markus G. Rudolph, Jason C. Cole, Michael Reutlinger, Christian Kramer, Hervé Schaffhauser, Agnès Nilly, Alexander Flohr, Bernd Kuhn	A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Faisal Malik, Zhijun Li	Is there a common allosteric binding site for G-protein coupled receptors?	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley	Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Wijitra Meelua, Julianna Oláh, Jitrayut Jitonnom	Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Xiao Liu, Lei Zheng, Chu Qin, John Z. H. Zhang, Zhaoxi Sun	Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Lorenzo Di Rienzo, Luca De Flaviis, Giancarlo Ruocco, Viola Folli, Edoardo Milanetti	Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu, Zhaoxi Sun	Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Roberto Paciotti, Cecilia Coletti, Alessandro Marrone, Nazzareno Re	The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Daniel Markthaler, Hamzeh Kraus, Niels Hansen	Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Phillip S. Hudson, Félix Aviat, Rubén Meana-Pañeda, Luke C. Warrensford, Benjamin C. Pollard, Samarjeet Prasad, Michael R. Jones, H. Lee Woodcock III, Bernard R. Brooks	Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Martin Amezcua, Jeffry Setiadi, Yunhui Ge, David L. Mobley	An overview of the SAMPL8 host-guest binding challenge.	J. Comput. Aided Mol. Des.	2022	DBLP DOI BibTeX RDF
9	Jialin Wu, Zhe Liu, Xiaofeng Yang, Zhanglin Lin	Improved compound-protein interaction site and binding affinity prediction using self-supervised protein embeddings.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Nelson R. C. Monteiro, Carlos J. V. Simões, Henrique V. Ávila, Maryam Abbasi, José Luís Oliveira, Joel P. Arrais	Explainable deep drug-target representations for binding affinity prediction.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Kai Sun, Xiuzhen Hu, Zhenxing Feng, Hongbin Wang, Haotian Lv, Ziyang Wang, Gaimei Zhang, Shuang Xu, Xiaoxiao You	Predicting Ca2+ and Mg2+ ligand binding sites by deep neural network algorithm.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Shaofu Lin, Chengyu Shi, Jianhui Chen	GeneralizedDTA: combining pre-training and multi-task learning to predict drug-target binding affinity for unknown drug discovery.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Jidong Zhang, Bo Liu, Zhihan Wang, Klaus Lehnert, Mark Gahegan	DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Sierra S. Nishizaki, Alan P. Boyle	SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Chenran Wang, Yang Chen, Yuan Zhang, Keqiao Li, Menghan Lin, Feng Pan, Wei Wu, Jinfeng Zhang	A reinforcement learning approach for protein-ligand binding pose prediction.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Anni A. Antikainen, Markus Heinonen, Harri Lähdesmäki	Modeling binding specificities of transcription factor pairs with random forests.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Vi Ngoc-Nha Tran, Alireza Shams, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli, Rafal Mostowy, Ted Cohen, Pia Abel zur Wiesch	vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
9	Rita Fioresi, P. Demurtas, G. Perini	Deep learning for MYC binding site recognition.	Frontiers Bioinform.	2022	DBLP DOI BibTeX RDF
9	Zhongliang Guo, Rui Yamaguchi	Machine learning methods for protein-protein binding affinity prediction in protein design.	Frontiers Bioinform.	2022	DBLP DOI BibTeX RDF
9	Rocco Meli, Garrett M. Morris, Philip C. Biggin	Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review.	Frontiers Bioinform.	2022	DBLP DOI BibTeX RDF
9	Vittoria Cicaloni, Malancha Karmakar, Luisa Frusciante, Francesco Pettini, Anna Visibelli, Maurizio Orlandini, Federico Galvagni, Maurizio Mongiat, Michael Silk, Federica Nardi, David B. Ascher, Annalisa Santucci, Ottavia Spiga	Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93.	Frontiers Bioinform.	2022	DBLP DOI BibTeX RDF
9	Federico Palazzetti, Cecilia Coletti, Alessandro Marrone, Fernando Pirani	Potential Energy Surfaces for Noble Gas (Ar, Kr, Xe, Rn)-Propylene Oxide Systems: Analytical Formulation and Binding.	Symmetry	2022	DBLP DOI BibTeX RDF
9	Luca Gagliardi, Andrea Raffo, Ulderico Fugacci, Silvia Biasotti, Walter Rocchia, Hao Huang 0003, Boulbaba Ben Amor, Yi Fang 0006, Yuanyuan Zhang, Xiao Wang, Charles Christoffer, Daisuke Kihara, Apostolos Axenopoulos, Stelios K. Mylonas, Petros Daras	SHREC 2022: Protein-ligand binding site recognition.	Comput. Graph.	2022	DBLP DOI BibTeX RDF
9	Soumiya Hamena, Souham Meshoul, Salima Ouadfel	Multi-descriptor approaches to oxygen binding proteins prediction and classification using deep learning.	Int. J. Bioinform. Res. Appl.	2022	DBLP DOI BibTeX RDF
9	Chaofeng Lou, Hongbin Yang, Jiye Wang, Mengting Huang, Weihua Li 0005, Guixia Liu, Philip W. Lee, Yun Tang 0001	IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Bin Sun 0005, Peter M. Kekenes-Huskey	Calmodulin's Interdomain Linker Is Optimized for Dynamics Signal Transmission and Calcium Binding.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Perumal Manivel, Parthiban Marimuthu, Sun Yu, Xiumin Chen	Multispectroscopic and Computational Investigations on the Binding Mechanism of Dicaffeoylquinic Acids with Ovalbumin.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Islem Hammami, Géraldine Farjot, Mikaël Naveau, Audrey Rousseaud, Thierry Prangé, Ira Katz, Nathalie Colloc'h	Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Santhosh Sankar, Naren Chandran Sakthivel, Nagasuma Chandra	Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Rory M. Crean, Christopher R. Pudney, David K. Cole, Marc van der Kamp	Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Gaurav Sharma, Lin Frank Song, Kenneth M. Merz Jr.	Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia	Hom-Complex-Based Machine Learning (HCML) for the Prediction of Protein-Protein Binding Affinity Changes upon Mutation.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Huiyan Lu, Yuji Komukai, Koto Usami, Yan Guo, Xinyue Qiao, Michiyoshi Nukaga, Tyuji Hoshino	Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Hiroko X. Kondo, Masanori Fujii, Takuma Tanioka, Yusuke Kanematsu, Takashi Yoshida, Yu Takano	Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Han Zhang 0028, Seonghoon Kim, Wonpil Im	Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Zheng Zhao, Lei Xie 0006, Philip E. Bourne	Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants".	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Agustín Ormazábal, Gustavo Pierdominici-Sottile, Juliana Palma	Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Bhagyesh Varvdekar, Akshay Prabhakant, Marimuthu Krishnan	Response of Terahertz Protein Vibrations to Ligand Binding: Calmodulin-Peptide Complexes as a Case Study.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Oliver B. Scott, Jing Gu, A. W. Edith Chan	Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Jorge Enrique Hernández González, Lucas N. Alberca, Yordanka Masforrol González, Osvaldo Reyes Acosta, Alan Talevi, Emir Salas-Sarduy	Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Austin M. Cool, Steffen Lindert	Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Steven R. Bowers, Dmitri K. Klimov, Christopher Lockhart	Mechanisms of Binding of Antimicrobial Peptide PGLa to DMPC/DMPG Membrane.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Daniela Trisciuzzi, Lydia Siragusa, Massimo Baroni, Gabriele Cruciani, Orazio Nicolotti	An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat Kumar Pal, Emilio Gallicchio	Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda	Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Xu Yan 0014, Yingfeng Lu, Zhen Li 0026, Qing Wei, Xin Gao 0001, Sheng Wang 0001, Song Wu, Shuguang Cui	PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Lingyan Wang, Kun Xi, Lizhe Zhu, Lin-Tai Da	DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Nisha Amarnath Jonniya, Parimal Kar	Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Emmanuel E. Moutoussamy, Hanif M. Khan, Mary F. Roberts, Anne Gershenson, Christophe Chipot, Nathalie Reuter	Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Shaoli Cui, Weijia Zhang, Xueguang Shao, Wensheng Cai	Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Qinghua Wang, Zhe Wang 0041, Sheng Tian, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou, Haiping Hao, Huiyong Sun	Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Nemanja Djokovic, Dusan Ruzic, Minna Rahnasto-Rilla, Tatjana Srdic-Rajic, Maija Lahtela-Kakkonen, Katarina Nikolic	Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Janez Konc, Samo Lesnik, Blaz Skrlj, Matej Sova, Matic Proj, Damijan Knez, Stanislav Gobec, Dusanka Janezic	ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Ebru Akkus, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak	Accurate Binding Free Energy Method from End-State MD Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Mohamed Marzouk Sobeh, Akio Kitao	Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Gian Marco Elisi, Laura Scalvini, Alessio Lodola, Marco Mor, Silvia Rivara	Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Janez Konc, Dusanka Janezic	ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Mert Golcuk, Aysima Hacisuleyman, Sema Zeynep Yilmaz, Elhan Taka, Ahmet Yildiz, Mert Gur	SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Vineeth R. Chelur, U. Deva Priyakumar	BiRDS - Binding Residue Detection from Protein Sequences Using Deep ResNets.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Vincenzo Laveglia, Andrea Giachetti 0002, Davide Sala, Claudia Andreini, Antonio Rosato	Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Md. Masud Rana 0008, Duc Duy Nguyen	EISA-Score: Element Interactive Surface Area Score for Protein-Ligand Binding Affinity Prediction.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Liping Zhou, Tingting Liu, Mengxia Mo, Yulong Shi, Leyun Wu, Yishui Li, Qiuping Qin, Weiliang Zhu, Chengkun Wu, Likun Gong, Zhijian Xu	Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Walter Fiedler, Fabian Freisleben, Jasmin Wellbrock, Karl N. Kirschner	Mebendazole's Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano	Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu 0001, Sheng-You Huang	Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Xiaocong Wang, Lihua Bie, Jun Gao	Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Guoqin Feng, Xiangying Zhang, Yan Li 0051, Renxiao Wang	Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Qingyu Li, Xiaochang Zhang, Lianlian Wu, Xiaochen Bo, Song He, Shengqi Wang	PLA-MoRe: A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Farideh Badichi Akher, Abdolkarim Farrokhzadeh, Neil Ravenscroft, Michelle M. Kuttel	Deciphering the Mechanism of Binding Selectivity of Chlorofluoroacetamide-Based Covalent Inhibitors toward L858R/T790M Resistance Mutation.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Maryam Ghasemitarei, Angela Privat-Maldonado, Maksudbek Yusupov, Shadi Rahnama, Annemie Bogaerts, Mohammad Reza Ejtehadi	Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Manuel A. Llanos, Clara Ventura, Pedro Martín, Nicolas Enrique, Juan I. Felice, Luciana Gavernet, Verónica Milesi	Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Raitis Bobrovs, Emils Edgars Basens, Laura Drunka, Iveta Kanepe, Sofija Matisone, Karlis Kristofers Velins, Victor Andrianov, Gundars Leitis, Diana Zelencova-Gopejenko, Dace Rasina, Aigars Jirgensons, Kristaps Jaudzems	Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Ilaria Salutari, Amedeo Caflisch	Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Shruti Koulgi, Archana Achalere, Uddhavesh Sonavane, Rajendra Joshi	Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Yanru Ji, Ying Fang, Jianhua Wu	Tension Enhances the Binding Affinity of β1 Integrin by Clamping Talin Tightly: An Insight from Steered Molecular Dynamics Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi	Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Ke Wang, Xueguang Shao, Wensheng Cai	Binding Models of Aβ42 Peptide with Membranes Explored by Molecular Simulations.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Carmen Domene, Leonardo Darré, Victoria Oakes, Saul Gonzalez-Resines	A Potential Route of Capsaicin to Its Binding Site in the TRPV1 Ion Channel.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF
9	Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot	Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.	J. Chem. Inf. Model.	2022	DBLP DOI BibTeX RDF