ZDOCK: An initial‐stage protein‐docking algorithm
Chen, Rong, Li, Li, Weng, Zhiping·2003·Proteins: Structure, Function, and Bioinformatics
Cited by (1,002)
Items 301–400 of 1,002
- The structure at 2 Å resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC–PC complexCarlos Contreras‐Martel, Adelio R. Matamala, Carola Bruna, German Poo-Caamaño, Daniel Eduardo Almonacid, Maximiliano Figueroa, José Martínez‐Oyanedel, Marta C. Bunster · 2006 · Biophysical Chemistry
- TOPK promotes lung cancer resistance to EGFR tyrosine kinase inhibitors by phosphorylating and activating c-JunYing Li, Zhiwei Yang, Weijie Li, Shudi Xu, Tao Wang, Ting Wang, Mengjie Niu, Shengli Zhang, Lintao Jia, Shengqing Li · 2016 · Oncotarget
- Interaction of E. coli Hsp90 with DnaK Involves the DnaJ Binding Region of DnaKAndrea N. Kravats, Shannon M. Doyle, Joel R. Hoskins, Olivier Genest, Erin E. Doody, Sue Wickner · 2016 · Journal of Molecular Biology
- CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein DockingRen Kong, Feng Wang, Jian Zhang, Fengfei Wang, Shan Chang · 2019 · Journal of Chemical Information and Modeling
- NMR structure of the viral peptide linked to the genome (VPg) of poliovirusCatherine H. Schein, Numan Oezguen, David E. Volk, Ravindranath Garimella, Aniko V. Paul, Werner A. Braun · 2006 · Peptides
- A new residue‐nucleotide propensity potential with structural information considered for discriminating protein‐RNA docking decoysChun Hua Li, Li Bin Cao, Ji Guo Su, Yong Xiao Yang, Cun Xin Wang · 2011 · Proteins Structure Function and Bioinformatics
- YESS 2.0, a Tunable Platform for Enzyme Evolution, Yields Highly Active TEV Protease VariantsCarl A. Denard, Chelsea Paresi, Rasha M. Yaghi, Natalie McGinnis, Zachary Bennett, Yi Li, George Georgiou, Brent L. Iverson · 2021 · ACS Synthetic Biology
- Deep learning for advancing peptide drug development: Tools and methods in structure prediction and designXinyi Wu, Huitian Lin, Renren Bai, Hongliang Duan · 2024 · European Journal of Medicinal Chemistry
- EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGFFarah Khayati, Laura Pérez‐Cano, Kamel Maouche, Aurélie Sadoux, Zineb Boutalbi, Marie-Pierre Podgorniak, Uwe Maskos, Niclas Setterblad, Anne Janin, Fabien M. Calvo et al. · 2015 · Oncotarget
- Predicting peptide binding sites on protein surfaces by clustering chemical interactionsChengfei Yan, Xiaoqin Zou · 2014 · Journal of Computational Chemistry
- Pairwise and Multimeric Protein–Protein Docking Using the LZerD Program SuiteJuan Esquivel‐Rodríguez, Vianney Filos-Gonzalez, Bin Li, Daisuke Kihara · 2014 · Methods in molecular biology
- Computational Methods for the Interaction between Cyclodextrins and Natural Compounds: Technology, Benefits, Limitations, and TrendsBotian Ding, Yuandong Yu, Sheng Geng, Benguo Liu, Youjin Hao, Guizhao Liang · 2022 · Journal of Agricultural and Food Chemistry
- Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signaturesYajie Wang, Vijay Alla, Deborah Goody, Shailendra K. Gupta, Alf Spitschak, Olaf Wolkenhauer A, Brigitte M. Pützer, David Engelmann · 2015 · Nucleic Acids Research
- The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptorsEduard Gracia, Daniel Farré, Antoni Cortés, Carles Ferrer‐Costa, Modesto Orozco, Josefa Mallol, Carme Lluı́s, Enric I. Canela, Peter James McCormick, Rafael Franco et al. · 2012 · The FASEB Journal
- A selective blocker of Kv1.2 and Kv1.3 potassium channels from the venom of the scorpion Centruroides suffusus suffususGerardo A. Corzo, Ferenc Papp, Zoltán Varga, Omar Barraza, Gerardo Pável Espino-Solís, Ricardo C. Rodŕıguez de la Vega, Rezsö Gáspár, György Panyi, Lourival Domingos Possani · 2008 · Biochemical Pharmacology
- High-resolution protein–protein docking by global optimization: recent advances and future challengesHahnbeom Park, Hasup Lee, Chaok Seok · 2015 · Current Opinion in Structural Biology
- Structure and Malonyl CoA-ACP Transacylase Binding of Streptomyces coelicolor Fatty Acid Synthase Acyl Carrier ProteinChristopher J. Arthur, Christopher Williams, Katherine Pottage, Eliza Płoskoń, Stuart C. Findlow, Steven G. Burston, Thomas James Simpson, Matthew P. Crump, John C. Crosby · 2009 · ACS Chemical Biology
- Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representationKazuhiro Takemura, Hao Guo, Shun Sakuraba, Nobuyuki Matubayasi, Akio Kitao · 2012 · The Journal of Chemical Physics
- Structural basis of the interactions between CXCR4 and CXCL12/SDF-1 revealed by theoretical approachesLei Xu, Youyong Li, Huiyong Sun, Dan Li, Tingjun Hou · 2013 · Molecular BioSystems
- Discrimination of near‐native structures in protein–protein docking by testing the stability of local minimaDima Kozakov, Ora Schueler‐Furman, Sándor Vajda · 2008 · Proteins Structure Function and Bioinformatics
- Predicting antibody complementarity determining region structures without classificationYoonjoo Choi, Charlotte Mary Deane · 2011 · Molecular BioSystems
- An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q BiosynthesisDanielle C. Lohman, Deniz Aydın, Helaina C. Von Bank, Robert Smith, Vanessa Linke, Erin Weisenhorn, Molly T. McDevitt, Paul D. Hutchins, Emily Wilkerson, Benjamin Wancewicz et al. · 2019 · Molecular Cell
- Psalmotoxin-1 Docking to Human Acid-sensing Ion Channel-1Yawar Jamal Qadri, Bakhrom K. Berdiev, Yuhua Song, Howard L. Lippton, Catherine M. Fuller, Dale John Benos · 2009 · Journal of Biological Chemistry
- SDOCK: A global protein‐protein docking program using stepwise force‐field potentialsChangsheng Zhang, Luhua Lai · 2011 · Journal of Computational Chemistry
- Interactions of IgG1 CH2 and CH3 Domains with FcRnTianlei Ying, Tina W. Ju, Yanping Wang, Ponraj Prabakaran, Dimiter Stanchev Dimitrov · 2014 · Frontiers in Immunology
- Tuning the serum persistence of human serum albumin domain III:diabody fusion proteinsVania E. Kenanova, Tove Olafsen, Felix B. Salazar, Lawrence E. Williams, Scott M. Knowles, Anna M. Wu · 2010 · Protein Engineering Design and Selection
- Antibodies binding the head domain of P2X4 inhibit channel function and reverse neuropathic painWendy A. Williams, John E. Linley, Clare A. Jones, Yoko Shibata, Arjan Snijder, James D. Button, Jonathan P. Hatcher, Ling Huang, Bruck Taddese, Peter Thornton et al. · 2019 · Pain
- Linear and Rationally Designed Stapled Peptides Abrogate TLR4 Pathway and Relieve Inflammatory Symptoms in Rheumatoid Arthritis Rat ModelAsma Achek, Masaud Shah, Ji Young Seo, Hyuk‐Kwon Kwon, Xiangai Gui, Hyeon‐Jun Shin, Eun-Young Cho, Byeong Sung Lee, Dong-Jin Kim, Sang Ho Lee et al. · 2019 · Journal of Medicinal Chemistry
- 2D Zernike polynomial expansion: Finding the protein-protein binding regionsE. Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Michele Monti, Giorgio Gosti, G. Ruocco · 2020 · Computational and Structural Biotechnology Journal
- Characterization of inhibitory mechanism and antifungal activity between group‐1 and group‐2 phytocystatins from taro (Colocasia esculenta)Ke‐Ming Wang, Senthil Kumar, Yi‐Sheng Cheng, Shripathi Venkatagiri, Ai‐Hwa Yang, Kai‐Wun Yeh · 2008 · FEBS Journal
- New benchmark metrics for protein‐protein docking methodsGao, Mu, Skolnick, Jeffrey · 2011 · Proteins: Structure, Function, and Bioinformatics
- Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter ComplexesYang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sándor Vajda · 2008 · PLoS Computational Biology
- PLVAP and GKN3 Are Two Critical Host Cell Receptors Which Facilitate Japanese Encephalitis Virus Entry Into NeuronsSriparna Mukherjee, Nabonita Sengupta, Ankur Chaudhuri, Irshad Akbar, Noopur Singh, Sibani Sen Chakraborty, Amol Ratnakar Suryawanshi, Arindam Bhattacharyya, Anirban Basu · 2018 · Scientific Reports
- Mapping of a Microbial Protein Domain Involved in Binding and Activation of the TLR2/TLR1 HeterodimerShuang Liang, Kavita B. Hosur, Shanyun Lu, Hesham F. Nawar, Benjamin R. Weber, Richard I. Tapping, Terry D Connell, George Hajishengallis · 2009 · The Journal of Immunology
- Memdock: an α-helical membrane protein docking algorithmHurwitz, Naama, Schneidman-Duhovny, Dina, Wolfson, Haim J. · 2016 · Bioinformatics
- Structural studies of human purine nucleoside phosphorylase: Towards a new specific empirical scoring functionLuís Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres, Ana Luiza Vivan, Lisandra M. Gava, Raquel Dias, Rodrigo Gay Ducati, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira de Azevedo · 2008 · Archives of Biochemistry and Biophysics
- Crystal structure of hexanoyl-CoA bound to β-ketoacyl reductase FabG4 of Mycobacterium tuberculosisDebajyoti Dutta, Sudipta Bhattacharyya, Amlan Roychowdhury, Rupam Biswas, Amit Kumar Das · 2012 · Biochemical Journal
- Pushing the accuracy limit of shape complementarity for protein-protein dockingYumeng Yan, Sheng‐You Huang · 2019 · BMC Bioinformatics
- Docking Paradigm in Drug DesignVladimir Borisovich Sulimov, Danil C. Kutov, Anna S. Taschilova, Ivan S. Ilin, Eugene Evgen'evich Tyrtyshnikov, Alexey V. Sulimov · 2020 · Current Topics in Medicinal Chemistry
- Germline IGHV3-53-encoded RBD-targeting neutralizing antibodies are commonly present in the antibody repertoires of COVID-19 patientsQ. Yan, P. He, Xiaohan Huang, K. Luo, Yu-Di Zhang, Haisu Yi, Qian Wang, Feng Li, Rui-Tian Hou, Xiaodi Fan et al. · 2021 · Emerging Microbes and Infections
- Evaluating template-based and template-free protein-protein complex structure predictionThom Vreven, Howook Hwang, Brian G. Pierce, Zhiping Weng · 2013 · Briefings in Bioinformatics
- A Conformationally Constrained Peptidomimetic Binds to the Extracellular Region of HER2 ProteinSashikanth Banappagari, Sharon Ronald, D. Seetharama Satyanarayanajois · 2010 · Journal of Biomolecular Structure and Dynamics
- Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targetsCarlos Jaime Camacho · 2005 · Proteins Structure Function and Bioinformatics
- Performance of the first protein docking server ClusPro in CAPRI rounds 3–5Stephen R. Comeau, Sándor Vajda, Carlos Jaime Camacho · 2005 · Proteins Structure Function and Bioinformatics
- Computational Reverse-Engineering of a Spider-Venom Derived Peptide Active Against Plasmodium falciparum SUB1Giacomo Bastianelli, Anthony Bouillon, Christophe Nguyen, Elodie Crublet, Stéphane Pêtres, Olivier Gorgette, Dung Le‐Nguyen, Jean-Christophe Barale, Michaël Nilges · 2011 · PLoS ONE
- Up-regulation of cytosolic tryparedoxin in Amp B resistant isolates of Leishmania donovani and its interaction with cytosolic tryparedoxin peroxidaseShashi Shekhar Suman, Asif Equbal, Amir Zaidi, Mohammad Yousuf Ansari, Krishn Pratap Singh, Kuljit Singh, Bidyut Purkait, Ganesh Chandra Sahoo, Sanjeeva Bimal, Pradeep Das et al. · 2015 · Biochimie
- Modeling Protein–Protein or Protein–DNA/RNA Complexes Using the HDOCK WebserverYumeng Yan, Sheng‐You Huang · 2020 · Methods in molecular biology
- A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking StudySrichandan Padhi, Samurailatpam Sanjukta, Rounak Chourasia, Rajendra Kumar Labala, Sudhir P. Singh, Amit K. Rai · 2021 · Frontiers in Molecular Biosciences
- Mechanical strain stimulates COPII‐dependent secretory trafficking via Rac1Santosh Phuyal, Elena Djaerff, Anabel‐Lise Le Roux, Martin J. Baker, Daniela Fankhauser, Sayyed Jalil Mahdizadeh, Veronika Reiterer, Amirabbas Parizadeh, Edward Felder, Jennifer Kahlhofer et al. · 2022 · The EMBO Journal
- Designing coarse grained-and atom based-potentials for protein-protein dockingDror Tobi · 2010 · BMC Structural Biology
- Structural complexity and functional diversity of plant NADPH oxidasesGurpreet Kaur, Kunchur Guruprasad, Brenda R. S. Temple, David G. Shirvanyants, Nikolay V. Dokholyan, Pratap Kumar Pati · 2017 · Amino Acids
- Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy functionChi Zhang, Song Liu, Yaoqi Zhou · 2005 · Proteins Structure Function and Bioinformatics
- Mycobacterium tuberculosis2004 · American Journal of Transplantation
- Optimal design of protein docking potentials: Efficiency and limitationsDror Tobi, İvet Bahar · 2005 · Proteins Structure Function and Bioinformatics
- Intron retention resulting from a silent mutation in the VWF gene that structurally influences the 5′ splice siteHamideh Yadegari, Arijit Biswas, Mohammad Suhail Akhter, Julia Driesen, Vytautas Ivaškevičius, Natascha Marquardt, Johannes Oldenburg · 2016 · Blood
- Consensus scoring for enriching near‐native structures from protein–protein docking decoysShide Liang, Samy O. Meroueh, Guangce Wang, Chao Qiu, Yaoqi Zhou · 2008 · Proteins Structure Function and Bioinformatics
- An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design ApproachesLinwei Li, Song‐Tao Liu, Wang Bi, Fei Liu, Shuhua Xu, Pirui Li, Yu Chen · 2023 · International Journal of Molecular Sciences
- Deciphering Fine Molecular Details of Proteins’ Structure and Function with a Protein Surface Topography (PST) MethodAnna D. Koromyslova, Anton O. Chugunov, Roman G. Efremov · 2014 · Journal of Chemical Information and Modeling
- Ranking protein–protein docking results using steered molecular dynamics and potential of mean force calculationsLaura J. Kingsley, Juan Esquivel‐Rodríguez, Ying Yang, Daisuke Kihara, Markus A. Lill · 2016 · Journal of Computational Chemistry
- The bacterial deubiquitinase Ceg23 regulates the association of Lys-63–linked polyubiquitin molecules on the Legionella phagosomeKelong Ma, Xiangkai Zhen, Biao Zhou, Ninghai Gan, Yang Cao, Chengpeng Fan, Songying Ouyang, Zhao‐Qing Luo, Jiazhang Qiu · 2020 · Journal of Biological Chemistry
- Assessment of protein–protein interfaces in cryo-EM derived assembliesSony Malhotra, Agnel Praveen Joseph, Jeyan Thiyagalingam, Maya Topf · 2021 · Nature Communications
- Identifying protein–protein interfacial residues in heterocomplexes using residue conservation scoresJingjing Li, De-Shuang Huang, Bing Wang, C. Chen · 2006 · International Journal of Biological Macromolecules
- Thioredoxin System from Deinococcus radioduransJosiah M. Obiero, Vanessa Pittet, Sara A. Bonderoff, David A. R. Sanders · 2009 · Journal of Bacteriology
- Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine MethyltransferaseFu, Weiqi, Liu, Nan, Qiao, Qi, Wang, Mingzhu, Min, Jinrong, Zhu, Bing, Xu, Rui-Ming, Yang, Na · 2016 · Journal of Biological Chemistry
- A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2Yuan‐Ming Zhang, Nan Zheng, Pei Hao, Ying Cao, Yang Zhong · 2005 · Computational Biology and Chemistry
- Nuclear Targeting of Methyl-Recycling Enzymes in Arabidopsis thaliana Is Mediated by Specific Protein InteractionsSang‐Hyun Lee, Andrew C. Doxey, Brendan J. McConkey, Barbara A. Moffatt · 2011 · Molecular Plant
- Homology Modeling and Docking Studies of Human Bcl-2L10 ProteinK Bhargavi, P. Chaitanya, Ramasree Dulapalli, Vasavi Malkhed, Dwarkanath K. Murthy, V. Uma · 2010 · Journal of Biomolecular Structure and Dynamics
- RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible moleculesÉmilie Neveu, Petr A. Popov, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron, Grégoire Danoy, Pascal Bouvry, Sergei Grudinin · 2018 · Bioinformatics
- Impact of plasma oxidation on structural features of human epidermal growth factorMaksudbek Yusupov, Jan‐Wilm Lackmann, Jamoliddin Razzokov, Surendra Kumar, Katharina Stapelmann, Annemie Bogaerts · 2018 · Plasma Processes and Polymers
- Breast cancer vaccination comes to age: impacts of bioinformaticsSepideh Parvizpour, Jafar Razmara, Yadollah Omidi · 2018 · Bioimpacts
- Search algorithms and scoring methods in protein-ligand dockingUmesh Yadava · 2018 · Endocrinology&Metabolism International Journal
- Zeta Inhibitory Peptide Disrupts Electrostatic Interactions That Maintain Atypical Protein Kinase C in Its Active Conformation on the Scaffold p62Li-Chun Lisa Tsai, Lei Xie, Kim Doré, Li Xie, Jason C. Del Rio, Charles C. King, Guillermo Martinez‐Ariza, Christopher Hulme, Roberto Malinow, Philip E. Bourne et al. · 2015 · Journal of Biological Chemistry
- Tumor suppressor p16INK4a inhibits cancer cell growth by down-regulating eEF1A2 through a direct interactionMee‐Hyun Lee, Bu Young Choi, Yong‐Yeon Cho, Sungyoung Lee, Zunnan Huang, Joydeb Kumar Kundu, Myoung Ok Kim, Dong Joon Kim, Ann M. Bode, Young‐Joon Surh et al. · 2013 · Journal of Cell Science
- USP36 stabilizes nucleolar Snail1 to promote ribosome biogenesis and cancer cell survival upon ribotoxic stressKewei Qin, Shuhan Yu, Yang Liu, Rongtian Guo, Shiya Guo, Junjie Fei, Yuemeng Wang, Kaiyuan Jia, Zhiqiang Xu, Hu Chen et al. · 2023 · Nature Communications
- Cobdock: an accurate and practical machine learning-based consensus blind docking methodSadettin Y. Ugurlu, David McDonald, Huangshu John Lei, Alan M. Jones, Shu Li, Henry Y. Tong, Mark S. Butler, Shan He · 2024 · Journal of Cheminformatics
- Automated antibody structure prediction using Accelrys tools: Results and best practicesMarc Fasnacht, Kenneth J. Butenhof, Anne Lamy, Francisco G. Hernandez-Guzman, Hongwei Huang, Lisa Yan · 2014 · Proteins Structure Function and Bioinformatics
- A Tumor-Penetrating Peptide Modification Enhances the Antitumor Activity of Thymosin Alpha 1Xingzhen Lao, Meng Liu, Jiao Chen, Heng Zheng · 2013 · PLoS ONE
- OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa L. ssp. indica), participates in stress adaptationJitendra Kumar Verma, Saurabh Gayali, Suchismita Dass, Amit Kumar, Shaista Parveen, Subhra Chakraborty, Niranjan Chakraborty · 2014 · Phytochemistry
- A possible S‐glutathionylation of specific proteins by glyoxalase II: An in vitro and in silico studyLuisa Ercolani, Andrea Scirè, Roberta Galeazzi, Luca Massaccesi, Laura Cianfruglia, Adolfo Amici, Francesco Piva, Lorena Urbanelli, Carla Emiliani, Giovanni Principato et al. · 2016 · Cell Biochemistry and Function
- Lipid metabolism potential and mechanism of CPe-III from chickpea (Cicer arietinum L.)Zhaohui Xue, Xiaonan Hou, Wancong Yu, Haichao Wen, Qian Zhang, Dan Li, Xiaohong Kou · 2017 · Food Research International
- Engineering a high-affinity humanized anti-CD24 antibody to target hepatocellular carcinoma by a novel CDR grafting designFumou Sun, Tong Wang, Jiahao Jiang, Yang Wang, Zhaoxiong Ma, Zhaoting Li, Yue Han, Mingzhu Pan, Jialing Cai, Min Wang et al. · 2017 · Oncotarget
- Protein–protein interactions of human glyoxalase II: findings of a reliable docking protocolRoberta Galeazzi, Emiliano Laudadio, Emanuele Falconi, Luca Massaccesi, Luisa Ercolani, Giovanna Mobbili, Cristina Minnelli, Andrea Scirè, Laura Cianfruglia, Tatiana Armeni · 2018 · Organic & Biomolecular Chemistry
- Structural insights on druggable hotspots in CD147: A bull's eye viewDhivya Kumar, Umashankar Vetrivel, Sowmya Parameswaran, Krishna Kumar Subramanian · 2019 · Life Sciences
- An environment-friendly chemical modification method for thiol groups on polypeptide macromolecules to improve the performance of regenerated keratin materialsBo Li, Yanli Sun, Jinbo Yao, Hailiang Wu, Yanqin Shen, Chao Zhi, Jiaying Li · 2022 · Materials & Design
- Protein-Protein Docking and Analysis Reveal That Two Homologous Bacterial Adenylyl Cyclase Toxins Interact with Calmodulin DifferentlyQing Guo, Justin E. Jureller, Julia T. Warren, Elena Solomaha, Jan Florián, Wei‐Jen Tang · 2008 · Journal of Biological Chemistry
- Detection of Phospho-Sites Generated by Protein Kinase CK2 in CFTR: Mechanistic Aspects of Thr1471 PhosphorylationAndrea Venerando, Cinzia Franchin, Natasha Cant, Giorgio Cozza, Mario Angelo Pagano, Kendra Tosoni, Ateeq Ahmed Al‐Zahrani, Giorgio Arrigoni, Robert C. Ford, Anil Mehta et al. · 2013 · PLoS ONE
- Modeling the structure of mAb 14B7 bound to the anthrax protective antigenArvind Sivasubramanian, Jennifer A. Maynard, Jeffrey J. Gray · 2007 · Proteins Structure Function and Bioinformatics
- Physicochemical and residue conservation calculations to improve the ranking of protein–protein docking solutionsYuhua Duan, Boojala Vijay B. Reddy, Yiannis N. Kaznessis · 2005 · Protein Science
- Flexible protein–protein docking with a multitrack iterative transformerChu, Lee‐Shin, Ruffolo, Jeffrey A., Harmalkar, Ameya, Gray, Jeffrey J. · 2024 · Protein Science
- Subangstrom Accuracy in pHLA-I Modeling by Rosetta FlexPepDock Refinement ProtocolTengfei Liu, Xianchao Pan, Li Chao, Wen Tan, Sujun Qu, Li Yang, Bochu Wang, Hu Mei · 2014 · Journal of Chemical Information and Modeling
- Protein−Protein Recognition Control by Modulating Electrostatic InteractionsSong Hee Han, Shijin Yin, Hong Yi, Stéphanie Mouhat, Su Qiu, Zhijian Cao, Jean‐Marc Sabatier, Yingliang Wu, Wenxin Li · 2010 · Journal of Proteome Research
- Inhibition Mechanism of the Acetylcholine Receptor by α-Neurotoxins as Revealed by Normal-Mode DynamicsAbraham O. Samson, Michael Levitt · 2008 · Biochemistry
- Familial Mediterranean Fever in Crete: a genetic and structural biological approach in a population of ‘intermediate risk’E. Fragouli, Elias Eliopoulos, E Petraki, Prodromos I. Sidiropoulos, Ivona A Aksentijevich, E. Galanakis, Heraklis D. Kritikos, Argyro Repa, George A Fragiadakis, DT Boumpas et al. · 2007 · Clinical Genetics
- Directed evolution of Tau class glutathione transferases reveals a site that regulates catalytic efficiency and masks co-operativityIrine Axarli, Abdi W. Muleta, Dimitriοs Vlachakis, Σοφία Κοσσίδα, Georgia A. Kotzia, Anastasios Maltezos, Prathusha Dhavala, Anastassios C. Papageorgiou, Nikolaos E. Labrou · 2015 · Biochemical Journal
- COARSE AND RELIABLE GEOMETRIC ALIGNMENT FOR PROTEIN DOCKINGY. WANG, Pankaj K. Agarwal, P. BROWN, Herbert Edelsbrunner, Johannes Rudolph · 2004 · Pacific Symposium on Biocomputing (PSB)
- A Docking Model Based on Mass Spectrometric and Biochemical Data Describes Phage Packaging Motor IncorporationFu, Chi-yu, Uetrecht, Charlotte, Kang, Sebyung, Morais, Marc C., Heck, Albert J.R., Walter, Mark R., Prevelige, Peter E. · 2010 · Molecular & Cellular Proteomics
- Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven dockingGiulini, Marco, Schneider, Constantin, Cutting, Daniel, Desai, Nikita, Deane, Charlotte M, Bonvin, Alexandre M J J · 2024 · Bioinformatics
- Recent Advances and Challenges in Protein Structure PredictionChunxiang Peng, Fang Liang, Yuhao Xia, Kailong Zhao, Minghua Hou, Guijun Zhang · 2023 · Journal of Chemical Information and Modeling
- Decrypting Prion Protein Conversion into a β-Rich Conformer by Molecular DynamicsNesrine Chakroun, Arianna Fornili, Stéphanie Prigent, Jens Kleinjung, Cecile Ayako Dreiss, Human Rezaei, Franca Fraternali · 2013 · Journal of Chemical Theory and Computation
- ASPDock: protein-protein docking algorithm using atomic solvation parameters modelLin Li, Da‐Chuan Guo, Yangyu Huang, Shiyong Liu, Yi Xiao · 2011 · BMC Bioinformatics