Predicting free energy changes using structural ensembles

Benedix, Alexander, Becker, Caroline M, de Groot, Bert L, Caflisch, Amedeo, Böckmann, Rainer A·2009·Nature Methods
DOI 10.1038/nmeth0109-3

Cited by (234)

Items 201–234 of 234

  1. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules
    Daniela Grimme, Domingo González-Ruiz, Holger Gohlke · 2012 · Royal Society of Chemistry eBooks
  2. A noninvasive approach to understanding adaptation, crop raiding behavior, and the fecal microbiota of the African elephant
    Tabitha Finch · 2013
  3. PPAC: Predicting Protein–Protein Affinity Changes Induced by Amino Acid Mutations Using Protein Large Language Models
    Leilei Zhang, Xiaofei Zhou, Lu Liang, Jianping Lin · 2025 · ACS Omega
  4. Categorization of hotspots into three types – weak, moderate and strong to distinguish protein–protein versus protein–peptide interactions
    A. Kiran Kumar, Ravindranath Singh Rathore · 2023 · Journal of Biomolecular Structure and Dynamics
  5. Constructing and Evaluating Predictive Models for Protein Biophysical Characteristics
    Michael A. Johnston, Jens Erik Nielsen · 2011 · Annual reports in computational chemistry
  6. SH3 Domain-Peptide Binding Energy Calculations Based on Structural Ensemble and Multiple Peptide Templates
    Seung Pyo Hong, Taesu Chung, Dongsup Kim · 2010 · PLoS ONE
  7. Protein Binding Interfaces and Their Binding Hot Spot Prediction: A Survey
    Qian Liu, Jinyan Li · 2013 · Translational bioinformatics
  8. Burial Level Change Defines a High Energetic Relevance for Protein Binding Interfaces
    Zhenhua Li, Ying He, Limsoon Wong, Jinyan Li · 2014 · IEEE Transactions on Computational Biology and Bioinformatics
  9. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules
    Franziska Bertelshofer, Liping Sun, Günther Greiner, Rainer A. Böckmann · 2015 · Frontiers in Bioengineering and Biotechnology
  10. Structured probabilistic models of proteins across spatial and fitness landscapes
    CHRISTOPHER JAMES LANGMEAD, Eric P. Xing, Hetunandan Kamichetty · 2011
  11. Identification of cytoplasmic sialidase NEU2-associated proteins by LC-MS/MS
    Secil Akyildiz Demir, Volkan Seyrantepe · 2018 · Turkish Journal of Biochemistry
  12. Tools for protein science
    Brian Matthews · 2017 · Protein Science
  13. From Computational Biophysics to Systems Biology (CBSB11) Celebrating Harold Scheragas 90th Birthday
    Paolo Carloni, Ulrich H. E. Hansmann, Sandipan Mohanty, Jeanne Meinke, Olav Zimmermann, Thomas Lippert, Wanessa Asfora Nadler · 2012
  14. Accounting for Target Flexibility During Ligand–Receptor Docking
    Simon Leis, Martin Zacharias · 2012 · Royal Society of Chemistry eBooks
  15. Prediction of protein mutation effects based on dehydration and hydrogen bonding – A large‐scale study
    Karen T. Schomburg, Eva Nittinger, Agnes Meyder, Stefan Bietz, Nadine Schneider, Gudrun Lange, Robert Klein, Matthias Rarey · 2017 · Proteins Structure Function and Bioinformatics
  16. A Workflow for the Prediction of the Effects of Residue Substitution on Protein Stability
    Ruben Acuña, Zoé Lacroix, Jacques Chomilier · 2013 · Lecture notes in computer science
  17. Importance of improving scoring methods in predicting protein free-energy changes
    Sen Liu · 2012 · IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI ...)
  18. From Sequence to Protein Folding Variations
    Jiaan Yang · 2019 · Biomedical Journal of Scientific & Technical Research
  19. Deciphering GB1’s Single Mutational Landscape: Insights from MuMi Analysis
    Guclu, Tandac F., Atilgan, Ali Rana, Atilgan, Canan · 2024 · The Journal of Physical Chemistry B
  20. Human pancreatic glucokinase. Structural and physico-chemical studies related to catalytic activation, kinetic cooperativity and GCK-diabetes.
    Janne Molnes · 2012 · NORA - Norwegian Open Research Archives
  21. Computational Tools and Databases for the Study and Characterization of Protein Interactions
    Joan Segura, Jose Ramon Blas Pastor, Narcís Fernández‐Fuentes · 2012 · IntechOpen eBooks
  22. Implicit Solvent Models and Electrostatics in Molecular Recognition
    Tyler Luchko, David Andrew Case · 2012
  23. Molecular modeling of the transmembrane domain of envelope glycoproteins from flaviviridae viruses
    Siti Azma Jusoh · 2010 · Publications of the UdS (Saarland University)
  24. Mechanisms of protein-protein association : atomistic molecular dynamics study of the association process
    Mazen Ahmad · 2012 · Publications of the UdS (Saarland University)
  25. Conformational selection and induced changes along the catalytic cycle of E. coli DHFR
    Thomas R. Weikl, David D. Boehr · 2012 · arXiv (Cornell University)
  26. Design of protein-protein interaction specificity using computational methods and experimental library screening
    T. Scott Chen · 2012 · DSpace@MIT (Massachusetts Institute of Technology)
  27. Bioquímica e biofísica computacionais: simulações da reatividade e da estrutura de biomoléculas
    Guilherme M. Arantes · 2016
  28. Computational analysis on protein binding and interactions-a water exclusion perspective
    Qian Liu · 2012
  29. Simulações computacionais de desenovelamento de proteína e complexação de ligantes com amostragem aumentada
    Ariane Nunes‐Alves · 2018
  30. In Silico Edgetic Profiling and Network Analysis of Human Genetic Variants, with an Application to Disease Module Detection
    Hongzhu Cui · 2020 · Digital WPI
  31. おしえて!全国脳神経疾患病棟 看護のくふう(第29回)尿漏れを防ぐアコーディオン式パッドの使用
    幸恵 武藤, 洋美 太田, 万里 磯部 · 2008 · ブレインナーシング
  32. Three types of hotspots- weak, moderate and strong in protein-protein and protein-peptide interactions
    A. Kiran Kumar, Ravindranath Singh Rathore · 2022
  33. Computational Prediction Approaches for Predicting Mutation Impact on Protein-Protein Interactions
    Yi Ping, Laura Hoekstra, K. Anton Feenstra · 2023 · Lecture notes on data engineering and communications technologies
  34. Additional file 1 of Improved thermostability of creatinase from Alcaligenes Faecalis through non-biased phylogenetic consensus-guided mutagenesis
    Bai, Xue, Li, Daixi, Ma, Fuqiang, Deng, Xi, Manjie Luo, Feng, Yan, Yang, Guangyu · 2020 · Figshare