Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
Zhou, Hongyi, Zhou, Yaoqi·2002·Protein Science
Cited by (901)
Items 401–500 of 901
- MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure modelsMarcin Pawlowski, Lukasz Pawel Kozlowski, Andrzej Kloczkowski · 2015 · Proteins Structure Function and Bioinformatics
- Robust prediction of mutation-induced protein stability change by property encoding of amino acidsSeungwoo Kang, G. Chen, Guosheng XIAO · 2008 · Protein Engineering Design and Selection
- Sorting protein decoys by machine-learning-to-rankXiaoyang Jing, Kai Wang, Ruqian Lu, Qiwen Dong · 2016 · Scientific Reports
- Effective knowledge‐based potentialsEvandro Ferrada, Francisco Melo · 2009 · Protein Science
- Building alternate protein structures using the elastic network modelQingyi Yang, Kim A. Sharp · 2008 · Proteins Structure Function and Bioinformatics
- Megazol and its bioisostere 4H-1,2,4-triazole: comparing the trypanocidal, cytotoxic and genotoxic activities and their in vitro and in silico interactions with the Trypanosoma brucei nitroreductase enzymeAlcione Silva de Carvalho, Kelly Salomão, Solange Lisboa de Castro, Taline Ramos Conde, Helena Pereira da Silva Zamith, Ernesto R. Caffarena, Belinda S. Hall, Shane R. Wilkinson, Núbia Boechat · 2014 · Memórias do Instituto Oswaldo Cruz
- Homology Modeling and Analysis of Structure Predictions of the Bovine Rhinitis B Virus RNA Dependent RNA Polymerase (RdRp)Devendra K. Rai, Elizabeth A. Rieder · 2012 · International Journal of Molecular Sciences
- Developments and Applications of Coil-Library-Based Residue-Specific Force Fields for Molecular Dynamics Simulations of Peptides and ProteinsFan Jiang, Haonan Wu, Wei Kang, Yun‐Dong Wu · 2019 · Journal of Chemical Theory and Computation
- Spatial distribution of disease-associated variants in three-dimensional structures of protein complexesA Gress, Vasily E. Ramensky, Olga V. Kalinina · 2017 · Oncogenesis
- Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: Chymotrypsin inhibitor 2 mutantsMichael Fernández, Julio Caballero, Leyden Fernández, José Ignacio Abreu, Miguel Garriga · 2007 · Journal of Molecular Graphics and Modelling
- Intramolecular surface contacts contain information about protein–protein interface regionsSjoerd J. de Vries, Alexandre M. J. J. Bonvin · 2006 · Bioinformatics
- Neuroinformatics analyses reveal GABAt and SSADH as major proteins involved in anticonvulsant activity of valproic acidSakshi Piplani, Prabhakar Kumar Verma, Ajit Kumar · 2016 · Biomedicine & Pharmacotherapy
- Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network modelsMichael T. Zimmermann, Sumudu P. Leelananda, Paweł Gniewek, Yaping Feng, Robert L. Jernigan, Andrzej Kloczkowski · 2011 · Journal of Structural and Functional Genomics
- Capturing native/native like structures with a physico-chemical metric (pcSM) in protein foldingAvinash Mishra, S. Srinivasa Rao, Aditya Mittal, Bhyravabhotla Jayaram · 2013 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
- Molecular Dynamics Simulations of the Mammalian Glutamate Transporter EAAT3Germano Heinzelmann, Serdar Kuyucak B · 2014 · PLoS ONE
- Identification of small-molecule ligands that bind to MiR-21 as potential therapeutics for endometriosis by screening ZINC database and in-vitro assaysSongping Liu, Yuxing Yang, Wei Li, Xin Tian, Hongyan Cui, Qiong Zhang · 2018 · Gene
- Structure Refinement of Membrane Proteins via Molecular Dynamics SimulationsBercem Dutagaci, Lim Heo, M. Feig · 2018 · Proteins: Structure, Function, and Bioinformatics
- In silico and in vitro analysis of boAP3d1 protein interaction with bovine leukaemia virus gp51Adriana P. Corredor-Figueroa, Janneth González, Luis Alfredo Baquero, Hernando Curtidor, Nury Nathalia Olaya-Galán, Manuel Alfonso Patarroyo, María Fernanda Gutiérrez · 2018 · PLoS ONE
- Spherical convolutions on molecular graphs for protein model quality assessmentIlia Igashov, Nikita Pavlichenko, Sergei Grudinin · 2021 · Machine Learning Science and Technology
- Information-Driven Docking for TCR-pMHC Complex PredictionThomas Peacock, Benny Chain · 2021 · Frontiers in Immunology
- Protein-Carbohydrate InteractionsAdeel Malik, Mohammad Hassan Baig, Balachandran Manavalan · 2018 · Elsevier eBooks
- Protein structure prediction using residue‐ and fragment‐environment potentials in CASP 11Hyungrae Kim, Daisuke Kihara · 2015 · Proteins Structure Function and Bioinformatics
- Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modelingGiacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini · 2019 · PLoS Computational Biology
- Empirical Potential Energy Function Toward ab Initio Folding G Protein-Coupled ReceptorsHongjie Wu, Huajing Ling, Lei Gao, Qiming Fu, Weizhong Lu, Yijie Ding, Min Jiang, Haiou Li · 2020 · IEEE Transactions on Computational Biology and Bioinformatics
- Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteomeTollefson, Mallory R., Gogal, Rose A., Weaver, A. Monique, Schaefer, Amanda M., Marini, Robert J., Azaiez, Hela, Kolbe, Diana L., Wang, Donghong, Weaver, Amy E., Casavant, Thomas L. et al. · 2023 · Human Genetics
- Improved performance in CAPRI round 37 using LZerD docking and template‐based modeling with combined scoring functionsLenna X. Peterson, Woong‐Hee Shin, Hyungrae Kim, Daisuke Kihara · 2017 · Proteins Structure Function and Bioinformatics
- Modeling CAPRI targets 110‐120 by template‐based and free docking using contact potential and combined scoring functionPetras J. Kundrotas, Ivan V. Anishchenko, Varsha D. Badal, Madhurima Das, T. A. Dauzhenka, Ilya A. Vakser · 2017 · Proteins Structure Function and Bioinformatics
- Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDockMieczyslaw Torchala, Tereza Gerguri, Raphaël A. G. Chaleil, Patrick Gordon, Francis Russell, Miriam Keshani, Paul A. Bates · 2019 · Proteins Structure Function and Bioinformatics
- GALT Protein Database, a Bioinformatics Resource for the Management and Analysis of Structural Features of a Galactosemia-Related Protein and Its MutantsAntonio d’Acierno, Angelo M. Facchiano, Anna Marabotti · 2009 · Genomics Proteomics & Bioinformatics
- From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact EstimationWeitao Sun, Jing J. He · 2011 · PLoS ONE
- Integrated prediction of the effect of mutations on multiple protein characteristicsMichael A. Johnston, Chresten R. Søndergaard, Jens Erik Nielsen · 2010 · Proteins Structure Function and Bioinformatics
- Limitations of Protein Structure Prediction Algorithms in Therapeutic Protein DevelopmentSarfaraz K. Niazi, Zamara Mariam, Rehan Zafar Paracha · 2024 · BioMedInformatics
- Template‐based and free modeling by RAPTOR++ in CASP8Jinbo Xu, Jian Peng, Feng Zhao · 2009 · Proteins Structure Function and Bioinformatics
- CONFORMATIONAL SAMPLING IN TEMPLATE-FREE PROTEIN LOOP STRUCTURE MODELING: AN OVERVIEWYaohang Li · 2013 · Computational and Structural Biotechnology Journal
- A multibody, whole‐residue potential for protein structures, with testing by Monte Carlo simulated annealingStefan Mayewski · 2005 · Proteins Structure Function and Bioinformatics
- SVR_CAF: An integrated score function for detecting native protein structures among decoysZhou Jianhong, Wenying Yan, Guang Hu, Bairong Shen · 2013 · Proteins Structure Function and Bioinformatics
- s DFIRE : Sequence‐specific statistical energy function for protein structure prediction by decoy selectionsMd Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou · 2016 · Journal of Computational Chemistry
- Human and server docking prediction for CAPRI round 30‐35 using LZerD with combined scoring functionsLenna X. Peterson, Hyungrae Kim, Juan Esquivel‐Rodríguez, Amitava Roy, Xusi Han, Woong‐Hee Shin, Jian Zhang, Genki Terashi, Matt Lee, Daisuke Kihara · 2016 · Proteins Structure Function and Bioinformatics
- The Role of the Active Site Flap in Streptavidin/Biotin Complex FormationNupur Bansal, Zheng Zheng, Lin Frank Song, Jun Pei, Kenneth M. Merz · 2018 · Journal of the American Chemical Society
- Interaction of Human Brain Acetylcholinesterase with Cyclophosphamide: A Molecular Modeling and Docking StudyShazi Shakil, Rosina Khan, Shams S. M. Tabrez, Qamre Alam, Nasimudeen R. Jabir, Mansour I. Sulaiman, Nigel H. Greig, Mohammad Amjad Kamal · 2011 · CNS & Neurological Disorders - Drug Targets
- SCUD: Fast structure clustering of decoys using reference state to remove overall rotationHongzhi Li, Yaoqi Zhou · 2005 · Journal of Computational Chemistry
- Protein Loop Modeling with Optimized Backbone Potential FunctionsShide Liang, Chi Zhang, Jamica Sarmiento, Daron M. Standley · 2012 · Journal of Chemical Theory and Computation
- Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinationsHongyi Zhou, Chi Zhang, S. Liu, Yaoqi Zhou · 2005 · Nucleic Acids Research
- A reduced protein model with accurate native‐structure identification abilityMarcos R. Betancourt · 2003 · Proteins Structure Function and Bioinformatics
- Surfaces: a software to quantify and visualize interactions within and between proteins and ligandsNatália Teruel, Vinícius Magalhães Borges, Rafaël Najmanovich · 2023 · Bioinformatics
- Another look at the conditions for the extraction of protein knowledge‐based potentialsMarcos R. Betancourt · 2008 · Proteins Structure Function and Bioinformatics
- MQAPRank: improved global protein model quality assessment by learning-to-rankXiaoyang Jing, Qiwen Dong · 2017 · BMC Bioinformatics
- Computational studies of protein–protein dissociation by statistical potential and coarse-grained simulations: a case study on interactions between colicin E9 endonuclease and immunity proteinsZhaoqian Su, Yinghao Wu · 2019 · Physical Chemistry Chemical Physics
- Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38‐46Charles W. Christoffer, Genki Terashi, Woong‐Hee Shin, Tunde W. Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Lenna X. Peterson, Jacob C. Verburgt, Daisuke Kihara · 2019 · Proteins Structure Function and Bioinformatics
- Identification of epitopes in Leptospira borgpetersenii leucine-rich repeat proteinsSupachai Nitipan, Tepyuda Sritrakul, Anthicha Kunjantarachot, Siriwan Prapong · 2012 · Infection Genetics and Evolution
- PSICA: a fast and accurate web service for protein model quality analysisWenbo Wang, Zhaoyu Li, Junlin Wang, Dong He Xu, Yi Shang · 2019 · Nucleic Acids Research
- Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation methodJiawen Chen, Zhong‐Ru Xie, Yinghao Wu · 2015 · Biomechanics and Modeling in Mechanobiology
- QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimizationZhigang Xu, Chi Zhang, Song Liu, Yaoqi Zhou · 2006 · Proteins Structure Function and Bioinformatics
- A knowledge‐based forcefield for protein–protein interface designLouis A. Clark, Herman van Vlijmen · 2007 · Proteins Structure Function and Bioinformatics
- Multi-level analysis of intrinsically disordered protein docking methodsJacob C. Verburgt, Zicong Zhang, Daisuke Kihara · 2022 · Methods
- Knowledge of Native Protein–Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding CandidatesPetr A. Popov, Sergei Grudinin · 2015 · Journal of Chemical Information and Modeling
- ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structuresJungkap Park, Kazuhiro Saitou · 2014 · BMC Bioinformatics
- A knowledge-based orientation potential for transcription factor-DNA dockingTakako Takeda, Rosario I. Corona, Jun‐tao Guo · 2012 · Bioinformatics
- Ligand-binding site prediction of proteins based on known fragment–fragment interactionsKota Kasahara, Kengo Kinoshita, Toshihisa Takagi · 2010 · Bioinformatics
- Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structuresJianzhao Gao, Yuedong Yang, Yaoqi Zhou · 2018 · BMC Bioinformatics
- Structural bases that underline Trypanosoma cruzi calreticulin proinfective, antiangiogenic and antitumor propertiesJaime Peña Álvarez, Jaime Teneb, Ismael Maldonado, Katherine Weinberger, Carlos Rosas, David Lemus A., Carolina Valck, Álvaro Olivera‐Nappa, Juan A. Asenjo, Arturo Ferreira · 2019 · Immunobiology
- Feature-based multiple models improve classification of mutation-induced stability changesLukas Folkman, Bela Stantić, Abdul Sattar · 2014 · BMC Genomics
- Sub-AQUA: real-value quality assessment of protein structure modelsYifeng David Yang, Preston Spratt, Hao Chen, Changsoon Park, Daisuke Kihara · 2010 · Protein Engineering Design and Selection
- A Structural-Based Strategy for Recognition of Transcription Factor Binding SitesBeisi Xu, Dustin E. Schones, Yongmei Wang, Haojun Liang, Guohui Li · 2013 · PLoS ONE
- Coarse Grained Modeling and Approaches to Protein FoldingCarlo Guardiani, Roberto Livi, Fabio Cecconi · 2010 · Current Bioinformatics
- Investigation of structural stability and functionality of homodimeric gramicidin towards peptide‐based drug: a molecular simulation approachG. Pavithrra, Ramalingam Rajasekaran · 2018 · Journal of Cellular Biochemistry
- Methods for Molecular Modelling of Protein ComplexesTejashree Rajaram Kanitkar, Neeladri Sen, Sanjana Anilkumar Nair, Neelesh Soni, Kaustubh Amritkar, Yogendra Ramtirtha, Mallur Srivatsan Madhusudhan · 2021 · Methods in molecular biology
- PSPP: A Protein Structure Prediction Pipeline for Computing ClustersMichael S. Lee, Rajkumar Bondugula, Valmik Desai, Nela Zavaljevski, In‐Chul Yeh, Anders Wallqvist, Jaques Reifman A · 2009 · PLoS ONE
- A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimatorsFederico Fogolari, Silvio C. E. Tosatto, Giorgio Colombo · 2005 · BMC Bioinformatics
- Contact‐assisted protein structure modeling by global optimization in CASP11Keehyoung Joo, InSuk Joung, Qianyi Cheng, Sung Jong Lee, Jooyoung Lee · 2015 · Proteins Structure Function and Bioinformatics
- AffinityVAE: A multi-objective model for protein-ligand affinity prediction and drug designMengying Wang, Weimin Li, Yu Xiao, Yin Luo, Ke Han, Can Wang, Qun Jin · 2023 · Computational Biology and Chemistry
- Efficiency improvement strategy of fuel cell system based on oxygen excess ratio and cathode pressure two-dimensional optimizationXingyi Ge, Kai Li, Wei Jun Tian, Renkang Wang, Xinming Wan, Hao Tang · 2024 · International Journal of Hydrogen Energy
- Structure refinement of protein model decoys requires accurate side‐chain placementMark A. Olson, Michael S. Lee · 2012 · Proteins Structure Function and Bioinformatics
- Conformational sampling and structure prediction of multiple interacting loops in soluble andβ-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo methodKe Tang, Samuel W. K. Wong, Jun S. Liu, Jinfeng Zhang, Jie Liang · 2015 · Bioinformatics
- The Contribution of Coevolving Residues to the Stability of KDO8P SynthaseSharon H. Ackerman, Domenico L. Gatti · 2011 · PLoS ONE
- Sequence statistics of tertiary structural motifs reflect protein stabilityFan Zheng, Gevorg Grigoryan · 2017 · PLoS ONE
- Protein structure model refinement in CASP12 using short and long molecular dynamics simulations in implicit solventGenki Terashi, Daisuke Kihara · 2017 · Proteins Structure Function and Bioinformatics
- IDP-LZerD: Software for Modeling Disordered Protein InteractionsCharles W. Christoffer, Daisuke Kihara · 2020 · Methods in molecular biology
- A distance‐dependent atomic knowledge‐based potential and force for discrimination of native structures from decoysMehdi Mirzaie, Changiz Eslahchi, Hamid Pezeshk, Mehdi Sadeghi · 2009 · Proteins Structure Function and Bioinformatics
- Homology modelling and molecular docking studies of human placental cadherin protein for its role in teratogenic effects of anti-epileptic drugsSakshi Piplani, Vandana Saini, Ravi Ranjan Kumar Niraj, Adya Pushp, Ajit Kumar · 2015 · Computational Biology and Chemistry
- Predicting mutant outcome by combining deep mutational scanning and machine learningHagit Sarfati, Si Naftaly, Niv Papo, Chen Keasar · 2021 · Proteins Structure Function and Bioinformatics
- Explicit Orientation Dependence in Empirical Potentials and Its Significance to Side-Chain ModelingJianpeng Ma · 2009 · Accounts of Chemical Research
- Scoring function accuracy for membrane protein structure predictionCen Gao, Harry A. Stern · 2007 · Proteins Structure Function and Bioinformatics
- Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle spaceYuedong Yang, Haiyan Liu · 2006 · Journal of Computational Chemistry
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictorsYu-Jen Lin, Arul S. Menon, Zhiqiang Hu, Steven E. Brenner · 2024 · Human Genomics
- LoopWeaver: Loop Modeling by the Weighted Scaling of Verified ProteinsDaniel Holtby, Shuai Cheng Li, Ming Li · 2013 · Journal of Computational Biology
- Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformationsPatrick Aloy, Baldomero Oliva · 2009 · BMC Structural Biology
- Self‐derived structure‐disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptidesJian Zhan, Husen Jia, Evgeny A. Semchenko, Yunqiang Bian, Amy M. Zhou, Zhixiu Li, Yuedong Yang, Jihua Wang, Sohinee Sarkar, Makrina Totsika et al. · 2018 · The FASEB Journal
- OPUS‐CSF: A C‐atom‐based scoring function for ranking protein structural modelsGang Xu, Tianqi Ma, Tianwu Zang, Qinghua Wang, Jianpeng Ma · 2017 · Protein Science
- A method for efficient calculation of thermal stability of proteins upon point mutationsBo Wang, Yifei Qi, Ya Gao, John Z. H. Zhang · 2020 · Physical Chemistry Chemical Physics
- RL-MLZerD: Multimeric protein docking using reinforcement learningTunde Aderinwale, Charles W Christoffer, D. Kihara · 2022 · Frontiers in Molecular Biosciences
- emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression modelShuang Yang, Weikang Gong, Tong Zhou, Xiaohan Sun, Lei Chen, Wenxue Zhou, Chunhua Li · 2023 · Briefings in Bioinformatics
- ICOSA: A Distance-Dependent, Orientation-Specific Coarse-Grained Contact Potential for Protein Structure ModelingWessam R. Elhefnawy, Lin Chen, Yun Hee Han, Yaohang Li · 2015 · Journal of Molecular Biology
- New computational method for prediction of interacting protein loop regionsMatthew L. Danielson, Markus A. Lill · 2010 · Proteins Structure Function and Bioinformatics
- Amino Acid Network for the Discrimination of Native Protein Structures from DecoysZhou Jianhong, Wenying Yan, Guang Hu, Bairong Shen · 2014 · Current Protein and Peptide Science
- In Silico Modeling of Human α2C-Adrenoreceptor Interaction with Filamin-2Marcin Pawlowski, Saras Saraswathi, Hanaa K. B. Motawea, Maqsood Ahmed Chotani, Andrzej Kloczkowski · 2014 · PLoS ONE
- Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atomsSandeep Chakraborty, Ravindra Venkatramani, Basuthkar Jagadeeshwar Rao, Bjarni Ásgeirsson, Abhaya M. Dandekar · 2013 · F1000Research
- Predicting flexible loop regions that interact with ligands: The challenge of accurate scoringMatthew L. Danielson, Markus A. Lill · 2011 · Proteins Structure Function and Bioinformatics
- Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical ModelsWoong‐Hee Shin, Xuejiao Kang, Jian Zhang, Daisuke Kihara · 2017 · Scientific Reports
- Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGIMarco Carraro, Giovanni Minervini, Manuel Giollo, Yana Bromberg, Emidio Capriotti, Rita Casadio, Roland L. Dunbrack, Lisa Elefanti, Piero Fariselli, Carlo Ferrari et al. · 2017 · Human Mutation