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 601–700 of 901

  1. Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia
    Aparna Natarajan, Thangarajan Rajkumar, Kesavan Sabitha · 2019 · Asian Pacific Journal of Cancer Prevention
  2. Molecular Phylogeny and Predicted 3D Structure of Plantbeta-D- N -Acetylhexosaminidase
    Md. Anowar Hossain, Hairul Azman Roslan · 2014 · The Scientific World JOURNAL
  3. Accelerating knowledge-based energy evaluation in protein structure modeling with Graphics Processing Units
    Ashraf S. Yaseen, Yaohang Li · 2011 · Journal of Parallel and Distributed Computing
  4. Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs
    Alejandro Panjkovich, Francisco Melo, Marc A. Martı́-Renom · 2008 · Genome biology
  5. Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation
    Anna Maria Bochicchio, Sandra Jordaan, Valeria Losasso, Shivan Chetty, Rodrigo Perera, Emiliano Ippoliti, Stefan Barth, Paolo Carloni · 2017 · Biomedicines
  6. All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds
    Majid Masso · 2017 · BioMed Research International
  7. Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction
    Xinxiang Wang, Sheng‐You Huang · 2019 · Journal of Chemical Information and Modeling
  8. Quality Assessment of Protein Docking Models Based on Graph Neural Network
    Ye Sun Han, Fei He, Yongbing Chen, Wenyuan Qin, Helong Yu, Dong He Xu · 2021 · Frontiers in Bioinformatics
  9. OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding
    Gang Xu, Qinghua Wang, Jianpeng Ma · 2021 · Bioinformatics
  10. Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19
    P. Chandra Sekar, E. Srinivasan, G. Chandrasekhar, Debarati Paul, G. Sanjay, S. Surya, NS. Arun Raj Kumar, Ramalingam Rajasekaran · 2022 · Journal of Molecular Modeling
  11. A distance‐ and orientation‐dependent energy function of amino acid key blocks
    Lin Chen, Jing J. He · 2013 · Biopolymers
  12. Prediction of Stability upon Point Mutation in the Context of the Folding Nucleus
    Mathieu Lonquety, Jacques Chomilier, Nikolaos C. Papandreou, Zoé Lacroix · 2010 · OMICS A Journal of Integrative Biology
  13. Topology-based potentials and the study of the competition between protein folding and aggregation
    Lidia Prieto, Antonio Rey · 2009 · The Journal of Chemical Physics
  14. Predicting transmembrane helix pair configurations with knowledge‐based distance‐dependent pair potentials
    Christina Wendel, Holger Gohlke · 2007 · Proteins Structure Function and Bioinformatics
  15. Distance‐dependent atomic knowledge‐based force in protein fold recognition
    Mehdi Mirzaie, Mehdi Sadeghi · 2011 · Proteins Structure Function and Bioinformatics
  16. Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models
    Mark A. Olson, Michael S. Lee · 2013 · Journal of Computational Chemistry
  17. Improving a Consensus Approach for Protein Structure Selection by Removing Redundancy
    Qingguo Wang, Yi Shang, Dong He Xu · 2011 · IEEE Transactions on Computational Biology and Bioinformatics
  18. Protein structural model selection based on protein-dependent scoring function
    Zhiquan He, Yi Shang, Dong He Xu, Yang Xu, Jingfen Zhang · 2012 · Statistics and Its Interface
  19. Protein structure prediction
    Deng Hai-You, Ya Jia, Yang Zhang · 2016 · Acta Physica Sinica
  20. Modeling protein-protein interactions with intrinsically disordered proteins
    Charles W. Christoffer, Daisuke Kihara · 2019 · Elsevier eBooks
  21. Microbial Fuels
    Farshad Darvishi, Serge Hiligsmann · 2017 · CRC Press eBooks
  22. Protein loop selection using orientation‐dependent force fields derived by parameter optimization
    Shide Liang, Chi Zhang, Daron M. Standley · 2011 · Proteins Structure Function and Bioinformatics
  23. A new clustering-based method for protein structure selection
    Qingguo Wang, Yi Shang, Dong He Xu · 2008 · International Joint Conference on Neural Networks (IJCNN)
  24. Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys
    Dan M Bolser, Ioannis Filippis, Henning Stehr, José M. Duarte, Michael Lappé · 2008 · BMC Structural Biology
  25. Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence
    Zhiwei Nie, Yiming Ma, Yutian Liu, Xiansong Huang, Zhihong Liu, Yang Peng, Fan Xu, Feng Yin, Zigang Li, Jie Fu et al. · 2025 · Briefings in Bioinformatics
  26. Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs , Model Ranking, and Deep Learning
    Yuki Kagaya, Tsukasa Nakamura, Jacob C. Verburgt, Anika Jain, Genki Terashi, Pranav Punuru, Emilia Tugolukova, Joon Hong Park, Anouka Saha, David Y. C. Huang et al. · 2025 · Proteins Structure Function and Bioinformatics
  27. Inactive ryanodine receptors sustain lysosomal availability for autophagy by promoting ER-lysosomal contact site formation
    Tim Vervliet, Jens Loncke, Marko Sever, Karan Ahuja, Chris Van den Haute, Tomas Luyten, Grace E. Stutzmann, Catherine M. Verfaillie, Tihomir Tomašič, Geert Bultynck · 2026 · Nature Communications
  28. On-line hierarchy of general linear models for selecting and ranking the best predicted protein structures
    Hani Z. Girgis, Jason J. Corso, D. Fischer · 2009 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  29. Applications of Normal Mode Analysis Methods in Computational Protein Design
    Vincent Frappier, Matthieu Chartier, Rafaël Najmanovich · 2016 · Methods in molecular biology
  30. Improving the hydrolysis and acyltransferase activity of bifunctional feruloyl esterases DLFae4 by multiple rational predictions and directed evolution
    Longxiang Li, Shengwei Sun, Mengxi Wang, Jiahui Xiang, Yuting Shao, Guojun Wu, Jingjie Zhou, Ummara Khan, Zhihong Xin · 2023 · Food Bioscience
  31. Designing evolvable libraries using multi-body potentials
    Michael Lappé, Ganesh Bagler, Ioannis Filippis, Henning Stehr, José M. Duarte, Rajagopal Sathyapriya · 2009 · Current Opinion in Biotechnology
  32. Computational analysis of androgen receptor (AR) variants to decipher the relationship between protein stability and related-diseases
    Fangfang Chen, Xiaoqing Chen, Fan Jiang, Feng Leng, Wei Yong Liu, Yaoting Gui, Jing Yu · 2020 · Scientific Reports
  33. Protposer: The web server that readily proposes protein stabilizing mutations with high PPV
    H. García-Cebollada, Alfonso López, J. Sancho · 2022 · Computational and Structural Biotechnology Journal
  34. Protein Structure Prediction by Protein Threading
    Ying Xu, Zhijie Liu, Liming Cai, Dong He Xu · 2007 · Biological and medical physics series
  35. In vivo folding efficiencies for mutants of the P22 tailspike β-helix protein correlate with predicted stability changes
    Lothar “Luther” Reich, Marion Becker, Robert Seckler, Thomas R. Weikl · 2009 · Biophysical Chemistry
  36. A Sampling-Based Method for Ranking Protein Structural Models by Integrating Multiple Scores and Features
    Xiaohu Shi, Jingfen Zhang, Zhiquan He, Yi Shang, Dong He Xu · 2011 · Current Protein and Peptide Science
  37. De novo sequencing and characterization of a novel Bowman–Birk inhibitor from Lathyrus sativus L. seeds by electrospray mass spectrometry
    Rachele Tamburino, Valeria Severino, Annamaria Sandomenico, Menotti Ruvo, Augusto Parente, Angela Chambery, Antimo Di Maro · 2012 · Molecular BioSystems
  38. SecStAnT: secondary structure analysis tool for data selection, statistics and models building
    Giuseppe Maccari, Giulia Lia Beatrice Spampinato, Valentina Tozzini · 2013 · Bioinformatics
  39. Stochastic Pairwise Alignments and Scoring Methods for Comparative Protein Structure Modeling
    Adam C. Marko, Kate A. Stafford, Troy Wymore · 2007 · Journal of Chemical Information and Modeling
  40. Can template-based protein models guide the design of sequence fitness for enhanced thermal stability of single domain antibodies?
    Mark A. Olson, Dan Zabetakis, Patricia M. Legler, Kendrick B. Turner, George P. Anderson, Ellen R. Goldman · 2015 · Protein Engineering Design and Selection
  41. Computational Evaluation of Protein Stability Change upon Mutations
    Shuangye Yin, Feng Ding, Nikolay V. Dokholyan · 2010 · Methods in molecular biology
  42. Molecular characterization of second tomato α1,3/4-fucosidase (α-Fuc’ase Sl-2), a member of glycosyl hydrolase family 29 active toward the core α1,3-fucosyl residue in plant N-glycans
    Md Ziaur Rahman, Yuta Tsujimori, Megumi Maeda, Md. Anowar Hossain, Takeshi Ishimizu, Yoshinobu Kimura · 2018 · The Journal of Biochemistry
  43. An information gain-based approach for evaluating protein structure models
    Guillaume Postic, Nathalie Janel, Pierre Tufféry, Gautier Moroy · 2020 · Computational and Structural Biotechnology Journal
  44. Loop Simulations
    Maxim M. Totrov · 2011 · Methods in molecular biology
  45. An in silico approach for structural and functional analysis of Heavy Metal Associated (HMA) proteins in Brassica oleracea
    Jasmin Šutković, Mujo Kekić, Maida Ljubijankic, Petar Glamočija · 2016 · Periodicals of Engineering and Natural Sciences (PEN)
  46. Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein–Protein Association
    Kalyani Dhusia, Zhaoqian Su, Yinghao Wu · 2020 · Biomolecules
  47. Towards Automating Protein Structure Determination from NMR Data
    Xin Gao · 2009 · UWSpace (University of Waterloo)
  48. iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines
    Nicolas Renaud, Yong Gyu Jung, Vasant Honavar, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue · 2020 · SoftwareX
  49. Custommune: a web tool to design personalized and population-targeted vaccine epitopes
    Mohammad Tarek, Mahmoud ElHefnawi, Juliana Terzi Maricato, Ricardo Sobhie Diaz, Iart Luca Shytaj, Andrea Savarino · 2020 · medRxiv
  50. GRAPE‐WEB: An automated computational redesign web server for improving protein thermostability
    Jinyuan Sun, Wenyu Shi, Zhihui Xing, Guomei Fan, Qinglan Sun, Linhuan Wu, Juncai Ma, Yinglu Cui, Bian Wu · 2024 · mLife
  51. United3D: A Protein Model Quality Assessment Program That Uses Two Consensus Based Methods
    Genki Terashi, Makoto Oosawa, Yuuki Nakamura, Kazuhiko Kanou, Mayuko Takeda‐Shitaka · 2012 · Chemical and Pharmaceutical Bulletin
  52. STP: The Sample-Train-Predict Algorithm and Its Application to Protein Structure Meta-Selection
    Jason J. Corso, Hani Z. Girgis · 2008
  53. Automated simulation-based membrane protein refinement into cryo-EM data
    Yvonnesdotter, Linnea, Rovšnik, Urška, Blau, Christian, Lycksell, Marie, Howard, Rebecca Joy, Lindahl, Erik · 2023 · Biophysical Journal
  54. Three enhancements to the inference of statistical protein‐DNA potentials
    Mohammed AlQuraishi, Harley H. McAdams · 2012 · Proteins Structure Function and Bioinformatics
  55. Assessment of Protein Structure Predictions
    Emidio Capriotti, Marc A. Martı́-Renom · 2008 · WORLD SCIENTIFIC eBooks
  56. New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures
    Xinxiang Wang, Di Zhang, Sheng‐You Huang · 2018 · Journal of Chemical Information and Modeling
  57. Absolute binding free energies of mucroporin and its analog mucroporin-M1 with the heptad repeat 1 domain and RNA-dependent RNA polymerase of SARS-CoV-2
    Felipe Rodrigues de Souza, Paloma Guimarães Moura, Rayla Kelly Magalhães Costa, Rudielson Santos Silva, André Silva Pimentel · 2022 · Journal of Biomolecular Structure and Dynamics
  58. GeoPacker : A novel deep learning framework for protein side‐chain modeling
    Jiale Liu, Changsheng Zhang, Luhua Lai · 2022 · Protein Science
  59. A new Hidden Markov Model for protein Quality Assessment using compatibility between protein sequence and structure
    Zhiquan He, Wenji Ma, Jingfen Zhang, Dong Qing Xu · 2014 · Tsinghua Science & Technology
  60. Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale
    Riccardo Capelli, Cristina Paissoni, Pietro Sormanni, Guido Tiana · 2014 · The Journal of Chemical Physics
  61. Design of a Rotamer Library for Coarse-Grained Models in Protein-Folding Simulations
    María Larriva, Antonio Rey · 2013 · Journal of Chemical Information and Modeling
  62. LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates
    Stewart E. Moughon, Ram Samudrala · 2011 · BMC Bioinformatics
  63. Prediction and Dissection of Protein-RNA Interactions by Molecular Descriptors
    Zhi-Ping Liu, Luonan Chen · 2015 · Current Topics in Medicinal Chemistry
  64. Molecular And 3D-Structural Characterization Of Fructose-1,6-Bisphosphate Aldolase Derived From Metroxylon Sagu
    Hairul Azman Roslan, Md. Anowar Hossain, Jerry Gerunsin · 2017 · Brazilian Archives of Biology and Technology
  65. The phosphorelay signal transduction system in Candida glabrata: an in silico analysis
    Natalee Carapia-Minero, Juan Arturo Castelán-Vega, Néstor O. Pérez, Aída Verónica Rodríguez-Tovar · 2017 · Journal of Molecular Modeling
  66. Exploring the conformational space for protein folding with sequential Monte Carlo
    Samuel W. K. Wong, Jun S. Liu, Samuel C. Kou · 2018 · The Annals of Applied Statistics
  67. MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials
    Tong Liu, Zheng Wang · 2020 · BMC Bioinformatics
  68. Improved Protein Decoy Selection via Non-Negative Matrix Factorization
    Nasrin Akhter, Kazi Lutful Kabir, Gopinath Chennupati, Raviteja Vangara, Boian S. Alexandrov, Hristo N. Djidjev, Amarda Shehu · 2021 · IEEE Transactions on Computational Biology and Bioinformatics
  69. Computer aided therapeutic tripeptide design, in alleviating the pathogenic proclivities of nocuous α-synuclein fibrils
    G. Chandrasekhar, E. Srinivasan, S. Nandhini, G. Pravallika, G. Sanjay, Ramalingam Rajasekaran · 2023 · Journal of Biomolecular Structure and Dynamics
  70. Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-Based Scoring Functions
    Bercem Dutagaci, Kitiyaporn Wittayanarakul, Takaharu Mori, M. Feig · 2017 · Journal of Chemical Theory and Computation
  71. Decoy selection for protein structure prediction via extreme gradient boosting and ranking
    Nasrin Akhter, Gopinath Chennupati, Hristo N. Djidjev, Amarda Shehu · 2020 · BMC Bioinformatics
  72. Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics—quantum and molecular mechanical approaches
    P. Chandra Sekar, Debarati Paul, E. Srinivasan, Ramalingam Rajasekaran · 2021 · Journal of Molecular Modeling
  73. Data‐assisted protein structure modeling by global optimization in CASP12
    Keehyoung Joo, Seungryong Heo, InSuk Joung, Seung Hwan Hong, Sung Jong Lee, Jooyoung Lee · 2018 · Proteins Structure Function and Bioinformatics
  74. Three-Dimensional Ideal Gas Reference State Based Energy Function
    Md Hoque, Avdesh Mishra · 2017 · Current Bioinformatics
  75. Structure Prediction of Protein Complexes
    Brian G. Pierce, Zhiping Weng · 2007 · Biological and medical physics series
  76. A model of local‐minima distribution on conformational space and its application to protein structure prediction
    Hongzhi Li · 2006 · Proteins Structure Function and Bioinformatics
  77. Assessment of protein folding potentials with an evolutionary method
    David De Sancho, Antonio Rey · 2006 · The Journal of Chemical Physics
  78. STRUCTURE PREDICTION OF HELICAL TRANSMEMBRANE PROTEINS AT TWO LENGTH SCALES
    Zhong Chen, Ying Xu · 2006 · Journal of Bioinformatics and Computational Biology
  79. Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation
    Hetunandan Kamisetty, Eric P. Xing, CHRISTOPHER JAMES LANGMEAD · 2007 · Springer eBooks
  80. Evolutionary method for the assembly of rigid protein fragments
    David De Sancho, Lidia Prieto, Ana M. Rubio, Antonio Rey · 2004 · Journal of Computational Chemistry
  81. Comparative Modeling of Drug Target Proteins
    Narayanan Eswar, Andrej Šali · 2007 · Elsevier eBooks
  82. De novo protein structure prediction by incremental inter-residue geometries prediction and model quality assessment using deep learning
    Jun Liu, Guang-Xing He, Kailong Zhao, Guijun Zhang · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  83. cgRNASP-CN: a minimal coarse-grained representation-based statistical potential for RNA 3D structure evaluation
    Ling Song, Shixiong Yu, Xunxun Wang, Ya-Lan Tan, Zhi-Jie Tan · 2022 · Communications in Theoretical Physics
  84. Protein intrachain contact prediction with most interacting residues (MIR)
    Ruben Acuña, Zoé Lacroix, Nikolaos C. Papandreou, Jacques Chomilier · 2014 · Bio-Algorithms and Med-Systems
  85. Large loop conformation sampling using the activation relaxation technique, ART‐nouveau method
    Jean‐François St‐Pierre, Normand Mousseau · 2012 · Proteins Structure Function and Bioinformatics
  86. Protein Structure Prediction Using Coarse-Grained Models
    Maciej Błaszczyk, Dominik Gront, Sebastian Kmiecik, Mateusz Kurciński, Michał Koliński, Maciej Paweł Ciemny, Katarzyna Ziółkowska, Marta Panek, Andrzej Koliński · 2018 · Springer series on bio- and neurosystems
  87. Identification and Functional Implications of the E5 Oncogene Polymorphisms of Human Papillomavirus Type 16
    Antonio Hunberto Silva-Júnior, Ruany Cristyne de Oliveira Silva, Ana Pavla Almeida Diniz Gurgel, Marconi Rêgo Barros Júnior, Kamylla Conceição Gomes Nascimento, Daffany Luana dos Santos, Lindomar Pena, Rita de Cássia Pereira Lima, Marcus Vinícius de Aragão Batista, Bárbara Simas Chagas et al. · 2024 · Tropical Medicine and Infectious Disease
  88. Genome-Wide Characterization and Expression Profiling of Phytosulfokine Receptor Genes (PSKRs) in Triticum aestivum with Docking Simulations of Their Interactions with Phytosulfokine (PSK): A Bioinformatics Study
    Hala Badr Khalil · 2024 · Genes
  89. Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine
    Yongtao Xu, Shui Yu, Jian‐Wei Zou, Guixiang Hu, Noorsaadah Abd Rahman, Rozana Othman, Xia Tao, Meilan Huang · 2015 · PLoS ONE
  90. Molecular characterization of tomato α1,3/4-fucosidase, a member of glycosyl hydrolase family 29 involved in the degradation of plant complex typeN-glycans
    Md Ziaur Rahman, Megumi Maeda, Satsuki Itano, Md. Anowar Hossain, Takeshi Ishimizu, Yoshinobu Kimura · 2016 · The Journal of Biochemistry
  91. Characterization of a metagenomic serine metalloprotease and molecular docking studies
    Kashif Shamim, Jaya Sharma, Milind C. Mutnale, Santosh Kumar Dubey, Sajiya Yusuf Mujawar · 2018 · Process Biochemistry
  92. OPUS‐SSF: A side‐chain‐inclusive scoring function for ranking protein structural models
    Gang Xu, Tianqi Ma, Qinghua Wang, Jianpeng Ma · 2019 · Protein Science
  93. Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy
    Cheng-Peng Zhou, Di Wang, Xiaoyong Pan, Hong‐Bin Shen · 2021 · International Journal of Molecular Sciences
  94. Molecular modelling of FtsZ proteins based on their homology in Escherichia coli and Mycobacterium tuberculosis as the key stage of rational design of new antituberculous compounds
    Oleg M. Demchuk, Pavel A. Karpov, Peter Raspor, Ya. B. Blume · 2011 · Acta Biologica Slovenica
  95. ITScorePro: An Efficient Scoring Program for Evaluating the Energy Scores of Protein Structures for Structure Prediction
    Sheng‐You Huang, Xiaoqin Zou · 2014 · Methods in molecular biology
  96. Sequence Tolerance of a Single-Domain Antibody with a High Thermal Stability: Comparison of Computational and Experimental Fitness Profiles
    Mark A. Olson, Patricia M. Legler, Dan Zabetakis, Kendrick B. Turner, George P. Anderson, Ellen R. Goldman · 2019 · ACS Omega
  97. Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38‐45
    Taeyong Park, Hyeonuk Woo, Minkyung Baek, Jinsol Yang, Chaok Seok · 2019 · Proteins Structure Function and Bioinformatics
  98. Evaluation of a mean field potential for protein folding with different interaction centers
    María Larriva, David De Sancho, Antonio Rey · 2006 · Physica A Statistical Mechanics and its Applications
  99. Modeling and Validation of Transmembrane Protein Structures
    Maya Schushan, Nir Ben‐Tal · 2010
  100. Correction: A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites
    Beisi Xu, Dustin E. Schones, Yongmei Wang, Haojun Liang, Guohui Li · 2013 · PLoS ONE