Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

Cited by (901)

Items 501–600 of 901

1. Meet Me Halfway: When Genomics Meets Structural Bioinformatics
   Sungsam Gong, Catherine L. Worth, Tammy M. K. Cheng, Tom L. Blundell · 2011 · Journal of Cardiovascular Translational Research
2. Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar
   Constanza Cárdenas, Axel Bidon‐Chanal, Pablo Conejeros, Gloria Arenas, Sergio H. Marshall, Francisco Javier Luque · 2010 · Journal of Computer-Aided Molecular Design
3. Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction
   Vagmita Pabuwal, Zhijun Li · 2008 · Protein Engineering Design and Selection
4. Substrate Access to the Active Sites in Aminopeptidase T, a Representative of a New Metallopeptidase Clan
   Sergey G. Odintsov, Izabela Sabała, Gleb P. Bourenkov, Vladimir Rybin, Matthias Bochtler · 2005 · Journal of Molecular Biology
5. SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles
   Marta Bueno, Carlos Jaime Camacho, Javier Sancho · 2007 · Proteins Structure Function and Bioinformatics
6. Self-Inhibitory Peptides Targeting the Neisseria gonorrhoeae MtrCDE Efflux Pump Increase Antibiotic Susceptibility
   Benjamin J. Evert, Valentin A. Slesarenko, Jilsy M. J. Punnasseril, T. Taha, Jian Zhan, Yaoqi Zhou, Evgeny A. Semchenko, Kate L. Seib · 2021 · Antimicrobial Agents and Chemotherapy
7. PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models
   Jun Xie, Youli Zhang, Ziyang Wang, Xiaocheng Jin, Xiaoli Lü, Shengxiang Ge, Xiaoping Min · 2025 · BMC Bioinformatics
8. Bioinformatic Analysis of Pathogenic Missense Mutations of Activin Receptor Like Kinase 1 Ectodomain
   Claudia Scotti, Carla Olivieri, Laura Boeri, Cecilia Canzonieri, Federica Ornati, Elisabetta Buscarini, Fabio Pagella, Cesare Danesino · 2011 · PLoS ONE
9. Fold prediction of VP24 protein of Ebola and Marburg viruses using de novo fragment assembly
   Michael S. Lee, Frank J. Lebeda, Mark A. Olson · 2009 · Journal of Structural Biology
10. An Atomistic Statistically Effective Energy Function for Computational Protein Design
    Christopher M. Topham, Sophie Barbe, Isabelle André · 2016 · Journal of Chemical Theory and Computation
11. Optimization of molecular docking scores with support vector rank regression
    Wei Wang, Wanlin He, Xi Fa Zhou, Xin Chen · 2013 · Proteins Structure Function and Bioinformatics
12. Evaluation of Unrestrained Replica-Exchange Simulations Using Dynamic Walkers in Temperature Space for Protein Structure Refinement
    Mark A. Olson, Michael S. Lee · 2014 · PLoS ONE
13. Molecular Dynamics Simulations Elucidate the Mechanism of Proton Transport in the Glutamate Transporter EAAT3
    Germano Heinzelmann, Serdar Kuyucak B · 2014 · Biophysical Journal
14. Mimicking the action of folding chaperones by Hamiltonian replica‐exchange molecular dynamics simulations: Application in the refinement of de novo models
    Hao Fan, Xavier Périole, Alan Edward Mark · 2012 · Proteins Structure Function and Bioinformatics
15. De Novo Protein Structure Prediction
    Ling‐Hong Hung, Shing-Chung Ngan, Ram Samudrala · 2007 · Biological and medical physics series
16. Research/Review: Insights into the Mutation-Induced Dysfunction of Arachidonic Acid Metabolism from Modeling of Human CYP2J2
    Xiaole Xia, Botao Fa, Shan Cong, Jingfang Wang, Kuo‐Chen Chou · 2014 · Current Drug Metabolism
17. GENN: A GEneral Neural Network for Learning Tabulated Data with Examples from Protein Structure Prediction
    Eshel Faraggi, Andrzej Kloczkowski · 2014 · Methods in molecular biology
18. Comparative Modeling of Drug Target Proteins☆
    Benjamin Webb, Narayanan Eswar, H. Fan, Natalia Khuri, Ursula Pieper, Guangwei Dong, Andrej Šali · 2014 · Elsevier eBooks
19. Refining near‐native protein–protein docking decoys by local resampling and energy minimization
    Shide Liang, Guangce Wang, Yaoqi Zhou · 2008 · Proteins Structure Function and Bioinformatics
20. Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials
    Sumudu P. Leelananda, Yaping Feng, Paweł Gniewek, Andrzej Kloczkowski, Robert L. Jernigan · 2010 · Springer eBooks
21. Methods for Accurate Homology Modeling by Global Optimization
    Keehyoung Joo, Jinwoo Lee, Jooyoung Lee · 2011 · Methods in molecular biology
22. Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach
    Michael Siderius, Filip Jagodzinski · 2017 · Journal of Computational Biology
23. The blind search for the closed states of hinge‐bending proteins
    Semen O. Yesylevskyy, Valery N. Kharkyanen, Alexander P. Demchenko · 2007 · Proteins Structure Function and Bioinformatics
24. SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening
    Yuanzhe Zhou, Yangwei Jiang, Shi‐Jie Chen · 2024 · Journal of Chemical Theory and Computation
25. A Practical Guide to Computational Tools for Engineering Biocatalytic Properties
    Aitor Vega, Antoni Planas, Xevi Biarnés · 2025 · International Journal of Molecular Sciences
26. A multilayer evaluation approach for protein structure prediction and model quality assessment
    Jingfen Zhang, Qingguo Wang, Kittinun Vantasin, Jiong Zhang, Zhiquan He, Ioan Kosztin, Yi Shang, Dong He Xu · 2011 · Proteins Structure Function and Bioinformatics
27. A simple probabilistic model of multibody interactions in proteins
    Kristoffer E. Johansson, Thomas Hamelryck · 2013 · Proteins Structure Function and Bioinformatics
28. Improved estimation of model quality using predicted inter-residue distance
    Lisha Ye, Peikun Wu, Zhenling Peng, Jianzhao Gao, Jian Liu, Jianyi Yang · 2021 · Bioinformatics
29. RNAdvisor: a comprehensive benchmarking tool for the measure and prediction of RNA structural model quality
    Bernard, Clement, Postic, Guillaume, Ghannay, Sahar, Tahi, Fariza · 2024 · Briefings in Bioinformatics
30. Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins
    Yunqi Li, Jianwen Fang · 2010 · Biochemical and Biophysical Research Communications
31. A natural unification of GNM and ANM and the role of inter-residue forces
    Hyuntae Na, Guang Song · 2014 · Physical Biology
32. Coarse-Grained Prediction of RNA Loop Structures
    Liang Liu, Shi‐Jie Chen · 2012 · PLoS ONE
33. Modeling Protein–Peptide Recognition Based on Classical Quantitative Structure–Affinity Relationship Approach: Implication for Proteome-Wide Inference of Peptide-Mediated Interactions
    Yang Zhou, Zhong Ni, Keping Chen, Haijun Liu, Liang Chen, Chaoqun Lian, Lirong Yan · 2013 · The Protein Journal
34. Normal mode analysis with molecular geometry restraints: Bridging molecular mechanics and elastic models
    Mingyang Lu, Jianpeng Ma · 2011 · Archives of Biochemistry and Biophysics
35. The non-additive contribution of hydroxyl substituents to Akt kinase–apigenin affinity
    Jian Lu, Zhuyi Zhang, Zhong Ni, Haijun Shen, Zhigang Tu, Hanqing Liu, Rongzhu Lu, Haifeng Shi · 2014 · Molecular Simulation
36. Determination of Pentapeptide Repeat Units in Qnr Proteins by the Structure-Based Alignment Approach
    Kwang Seung Park, Jung Hun Lee, Da Un Jeong, Jae Jin Lee, Xing Wu, Byeong Chul Jeong, Choong-Min Kang, Sang Hee Lee · 2011 · Antimicrobial Agents and Chemotherapy
37. A Constraint Solver for Flexible Protein Model
    Federico Campeotto, Alessandro Dal Palù, Agostino Dovier A, Ferdinando Fioretto, Enrico Pontelli · 2013 · Journal of Artificial Intelligence Research
38. Novel Nonlinear Knowledge-Based Mean Force Potentials Based on Machine Learning
    Q. Dong, Shuigeng Zhou · 2011 · IEEE/ACM Transactions on Computational Biology & Bioinformatics
39. Incorporating Ab Initio energy into threading approaches for protein structure prediction
    Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Cheng Li, Wei‐Mou Zheng, Dongbo Bu · 2011 · BMC Bioinformatics
40. Force Fields for Homology Modeling
    Andrew J. Bordner · 2011 · Methods in molecular biology
41. ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment
    Zhongwang Yu, Yuangen Yao, Haiyou Deng, Ming Yi · 2019 · BMC Bioinformatics
42. Statistical potentials for 3D structure evaluation: From proteins to RNAs*
    Ya-Lan Tan, Chenjie Feng, Xunxun Wang, Wenbing Zhang, Zhi-Jie Tan · 2020 · Chinese Physics B
43. Domain-Based Protein Docking with Extremely Large Conformational Changes
    Charles W. Christoffer, Daisuke Kihara · 2022 · Journal of Molecular Biology
44. Computational design of glutamate dehydrogenase in Bacillus subtilis natto
    Lili Chen, Jiale Wang, Yu Hu, Bing-Jun Qian, Xiaomin Yao, Jianhua Zhang, Jianhua Zhang · 2013 · Journal of Molecular Modeling
45. Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativa L.)
    Chhavi Dawar, Sunita Jain, Sudhir Kumar · 2013 · Journal of Molecular Modeling
46. A Knowledge-Based Potential with an Accurate Description of Local Interactions Improves Discrimination between Native and Near-Native Protein Conformations
    Evandro Ferrada, Ismael A. Vergara, Francisco Melo · 2007 · Cell Biochemistry and Biophysics
47. QM/MM–PB/SA scoring of the interaction strength between Akt kinase and apigenin analogues
    Jian Lu, Zhuyi Zhang, Zhong Ni, Haijun Shen, Zhigang Tu, Hanqing Liu, Rongzhu Lu · 2014 · Computational Biology and Chemistry
48. Fingerprinting protein structures effectively and efficiently
    Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li · 2013 · Bioinformatics
49. Discrete structural features among interface residue-level classes
    Gopichandran Sowmya, Shoba Ranganathan · 2015 · BMC Bioinformatics
50. Exploration of the binding modes of l-asparaginase complexed with its amino acid substrates by molecular docking, dynamics and simulation
    Rajeswara Reddy Erva, Satish Babu Rajulapati, Chandrasai Potla Durthi, Madhuri Pola · 2016 · 3 Biotech
51. Protein Refolding in Silico with Atom-based Statistical Potentials and Conformational Search Using a Simple Genetic Algorithm
    Qiaojun Fang, David Shortle · 2006 · Journal of Molecular Biology
52. Nonbonded terms extrapolated from nonlocal knowledge‐based energy functions improve error detection in near‐native protein structure models
    Evandro Ferrada, Francisco Melo · 2007 · Protein Science
53. Computational Assessment of Protein–Protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes
    Bo Wang, Zhaoqian Su, Yinghao Wu · 2021 · Genomics Proteomics & Bioinformatics
54. lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures
    Tarafder, Sumit, Bhattacharya, Debswapna · 2024 · Journal of Chemical Information and Modeling
55. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction
    Myong‐Ho Chae, Florian Krull, Ernst‐Walter Knapp · 2015 · Proteins Structure Function and Bioinformatics
56. PUDGE: a flexible, interactive server for protein structure prediction
    Raquel Norel, Donald S. Petrey, Barry H. Honig · 2010 · Nucleic Acids Research
57. Evaluation system and web infrastructure for the second cryo-EM model challenge
    Andriy Kryshtafovych, Paul D. Adams, Catherine L. Lawson, Wah Chiu · 2018 · Journal of Structural Biology
58. Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD
    Charles W. Christoffer, Daisuke Kihara · 2022 · PROTEOMICS
59. Mapping the energy landscape of PROTAC-mediated protein-protein interactions
    José A. Villegas, Tasneem M. Vaid, Michael E. Johnson, Terry W. Moore · 2023 · Computational and Structural Biotechnology Journal
60. Structure-based prediction of transcription factor binding sites
    Jun‐tao Guo, Shane Lofgren, Alvin Farrel · 2014 · Tsinghua Science & Technology
61. Improvement in Low-Homology Template-Based Modeling by Employing a Model Evaluation Method with Focus on Topology
    Wentao Dai, Tingrui Song, Xuan Wang, Xiaoyang Jin, Lizong Deng, Aiping Wu, Taijiao Jiang · 2014 · PLoS ONE
62. QA-RecombineIt: a server for quality assessment and recombination of protein models
    Marcin Pawlowski, Albert Bogdanowicz, Janusz Marek Bujnicki · 2013 · Nucleic Acids Research
63. Interdomain compactization in human tyrosyl-tRNA synthetase studied by the hierarchical rotations technique
    Semen O. Yesylevskyy, Oleksandr V. Savytskyi, K. A. Odynets, Alexander I. Kornelyuk · 2011 · Biophysical Chemistry
64. Using Structure to Explore the Sequence Alignment Space of Remote Homologs
    Andrew Kuziemko, Barry H. Honig, Donald S. Petrey · 2011 · PLoS Computational Biology
65. Understanding TR Binding to pMHC Complexes: How Does a TR Scan Many pMHC Complexes yet Preferentially Bind to One
    Javed Mohammed Khan, Shoba Ranganathan · 2011 · PLoS ONE
66. Scoring Functions for De Novo Protein Structure Prediction Revisited
    Shing-Chung Ngan, Ling‐Hong Hung, Tianyun Liu, Ram Samudrala · 2008 · Humana Press eBooks
67. Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control
    Sebastian Raschka, Anne M. Scott, Nan Liu, Santosh Gunturu, Mar Huertas, Weiming Li, Leslie A. Kuhn · 2018 · Journal of Computer-Aided Molecular Design
68. Activity of select dehydrogenases with Sepharose-immobilized N6-carboxymethyl-NAD
    Justin Beauchamp, Claire Vieille · 2015 · Bioengineered
69. Detecting local residue environment similarity for recognizing near‐native structure models
    Hyungrae Kim, Daisuke Kihara · 2014 · Proteins Structure Function and Bioinformatics
70. Identification of DNA-binding protein target sequences by physical effective energy functions, free energy analysis of lambda repressor-DNA complexes
    Elisabetta Moroni, Michele Caselle, Federico Fogolari · 2007 · BMC Structural Biology
71. Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom
    Avdesh Mishra, Sumaiya Iqbal, Md Tamjidul Hoque · 2016 · Journal of Theoretical Biology
72. Fast de novo discovery of low‐energy protein loop conformations
    Samuel W. K. Wong, Jun S. Liu, Samuel C. Kou · 2017 · Proteins Structure Function and Bioinformatics
73. FOLD HELICAL PROTEINS BY ENERGY MINIMIZATION IN DIHEDRAL SPACE AND A DFIRE-BASED STATISTICAL ENERGY FUNCTION
    Hongzhi Li, Yaoqi Zhou · 2005 · Journal of Bioinformatics and Computational Biology
74. Docking and Scoring in Drug Discovery
    Francesca Spyrakis, Pietro Cozzini, Glen E. Kellogg · 2010 · Wiley eBooks
75. Advances in Peptide/Protein Structure Prediction Tools and their Relevance for Structural Biology in the Last Decade
    Samilla Beatriz de Rezende, Lucas Rodrigues de Lima, Maria Lı́gia Rodrigues Macedo, Octávio Luiz Franco, Marlon Henrique e Silva Cardoso · 2023 · Current Bioinformatics
76. Application of Hydration Thermodynamics to the Evaluation of Protein Structures and Protein-Ligand Binding
    Yuichi Harano · 2012 · Entropy
77. Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection
    Jun Pei, Zheng Zheng, Kenneth M. Merz · 2019 · Journal of Chemical Information and Modeling
78. Hydrogen bonds in anoplin peptides aid in identification of a structurally stable therapeutic drug scaffold
    Shruti Sunil Ranade, Ramalingam Rajasekaran · 2020 · Journal of Molecular Modeling
79. Assessing how multiple mutations affect protein stability using rigid cluster size distributions
    Erik Andersson, Rebecca Hsieh, Szeto Howard, Roshanak Farhoodi, Nurit Haspel, Filip Jagodzinski · 2016 · IEEE International Conference on Computational Advances in Bio and Medical Sciences
80. Development of a New Benchmark for Assessing the Scoring Functions Applicable to Protein–Protein Interactions
    Li Han, Qifan Yang, Zhihai Liu, Yan Li, Renxiao Wang · 2018 · Future Medicinal Chemistry
81. Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling
    Sergei V Rakhmanov, Vsevolod J. Makeev · 2007 · BMC Structural Biology
82. Threading without optimizing weighting factors for scoring function
    Yifeng David Yang, Changsoon Park, Daisuke Kihara · 2008 · Proteins Structure Function and Bioinformatics
83. Two New Heuristic Methods for Protein Model Quality Assessment
    Wenbo Wang, Junlin Wang, Dong He Xu, Yi Shang · 2018 · IEEE Transactions on Computational Biology and Bioinformatics
84. Unsupervised and Supervised Learning over the Energy Landscape for Protein Decoy Selection
    Nasrin Akhter, Gopinath Chennupati, Kazi Lutful Kabir, Hristo N. Djidjev, Amarda Shehu · 2019 · Biomolecules
85. A knowledge-based structure-discriminating function that requires only main-chain atom coordinates
    Yoshihide Makino, Nobuya Itoh · 2008 · BMC Structural Biology
86. Benchmarking of TASSER in the ab initio limit
    Jose M. Borreguero, Jeffrey Skolnick · 2007 · Proteins Structure Function and Bioinformatics
87. Template‐free modeling by LEE and LEER in CASP 11
    InSuk Joung, Sun Young Lee, Qianyi Cheng, Jong Yun Kim, Keehyoung Joo, Sung Jong Lee, Jooyoung Lee · 2015 · Proteins Structure Function and Bioinformatics
88. Improving the orientation-dependent statistical potential using a reference state
    Yufeng Liu, Jianyang Zeng, Haipeng Gong · 2014 · Proteins Structure Function and Bioinformatics
89. Robust Prediction of Single and Multiple Point Protein Mutations Stability Changes
    Óscar Álvarez-Machancoses, Enrique J. deAndrés‐Galiana, Juan Luis Fernández‐Martínez, Andrzej Kloczkowski · 2019 · Biomolecules
90. Molecular and thermodynamic mechanisms for protein adaptation
    Qinyi Zhao · 2022 · European Biophysics Journal
91. On the Importance of the Distance Measures Used to Train and Test Knowledge-Based Potentials for Proteins
    Martin Carlsen, Patrice Koehl, Peter Røgen · 2014 · PLoS ONE
92. Computational prediction and analysis of the DR6–NAPP interaction
    Sergei Y. Ponomarev, Joseph Audie · 2010 · Proteins Structure Function and Bioinformatics
93. Knowledge-based potentials in protein fold recognition
    Mehdi Mirzaie, Mehdi Sadeghi · 2010 · Archives of Advances in Biosciences
94. Non-Negative Matrix Factorization for Selection of Near-Native Protein Tertiary Structures
    Nasrin Akhter, Raviteja Vangara, Gopinath Chennupati, Boian S. Alexandrov, Hristo N. Djidjev, Amarda Shehu · 2019 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
95. Prediction of Protein Tertiary Structures Using MUFOLD
    Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan Kosztin, Yi Shang, Dong He Xu · 2011 · Methods in molecular biology
96. In Silico Design of a Poly-epitope Vaccine for Urinary Tract Infection Based on Conserved Antigens by Modern Vaccinology
    Maryam Javadi, Mana Oloomi, Saeid Bouzari · 2020 · International Journal of Peptide Research and Therapeutics
97. Energy minimizations with a combination of two knowledge‐based potentials for protein folding
    David De Sancho, Antonio Rey · 2008 · Journal of Computational Chemistry
98. A Free-Rotating and Self-Avoiding Chain Model for Deriving Statistical Potentials Based on Protein Structures
    Ji Cheng, Jianfeng Pei, Luhua Lai · 2007 · Biophysical Journal
99. Synergistic Anti-Cancer Activity of Melittin and Erlotinib in Non-Small Cell Lung Cancer
    Hairul-Islam Mohamed Ibrahim, Jihad Alessa, Hala Badr Khalil, Gamal Mahmoud Bekhet, Ashraf Y.Z. Khalifa · 2025 · International Journal of Molecular Sciences
100. Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics
     Semin Lee, Alan Brown, William R. Pitt, Alícia P. Higueruelo, Sungsam Gong, G. Richard Bickerton, Adrian M. Schreyer, Duangrudee Tanramluk, Alison J. Baylay, Tom L. Blundell · 2009 · Molecular BioSystems