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Chemistry

D-Index
81
Citations
25516
World Ranking
3216
National Ranking
41

Overview

Ulf Ryde is affiliated with Lund University in Sweden and has contributed extensively to the field of Biochemistry, Genetics, and Molecular Biology, with a particular focus on Molecular Biology, Renewable Energy, Sustainability and the Environment, Materials Chemistry, Inorganic Chemistry, and Catalysis. Their research addresses fundamental questions primarily involving metalloenzymes and iron-sulfur proteins, enzyme structure and function, protein structure and dynamics, ammonia synthesis and nitrogen reduction, metal-catalyzed oxygenation mechanisms, advanced chemical physics studies, and electrocatalysts for energy conversion.

Ryde has published research in several scientific journals, with frequent contributions to:

  • Inorganic Chemistry
  • Journal of Chemical Theory and Computation
  • JBIC Journal of Biological Inorganic Chemistry
  • Dalton Transactions
  • Acta Crystallographica Section D Structural Biology

Notable recent papers authored by or involving Ryde include:

  • "On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies" (2021), Journal of Chemical Theory and Computation
  • "What Is the Structure of the E4 Intermediate in Nitrogenase?" (2020), Journal of Chemical Theory and Computation
  • "Entropy-Entropy Compensation between the Protein, Ligand, and Solvent Degrees of Freedom Fine-Tunes Affinity in Ligand Binding to Galectin-3C" (2021), JACS Au
  • "Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands" (2021), JBIC Journal of Biological Inorganic Chemistry
  • "Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand" (2020), Journal of Catalysis

Throughout their career, Ryde has collaborated frequently with several researchers, indicating active engagement in cooperative scientific efforts. Key coauthors include:

  • Esko Oksanen
  • Hao Jiang
  • Lili Cao
  • Mehdi Irani
  • Sonia Jafari

The main themes in Ryde's scientific work highlight exploration of enzyme mechanisms, protein-ligand interactions, and catalytic processes relevant to both biological and environmental chemistry. Their contributions intersect with both fundamental biochemical systems and applied topics in sustainability and energy conversion.

Best Publications

  • The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

    Samuel Genheden;Ulf Ryde

  • Molcas: a program package for computational chemistry.

    Gunnar Karlström;Roland Lindh;Per-Åke Malmqvist;Björn O Roos

  • COMPARISON OF METHODS FOR DERIVING ATOMIC CHARGES FROM THE ELECTROSTATIC POTENTIAL AND MOMENTS

    Emma Sigfridsson;Ulf Ryde

  • Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

    Ulf Ryde;Pär Söderhjelm

  • Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field

    Aaron Weis;Kambiz Katebzadeh;Pär Söderhjelm;Ingemar Nilsson

  • Performance of density functionals for first row transition metal systems

    Kasper P. Jensen;Björn O. Roos;Ulf Ryde

  • Structure, strain, and reorganization energy of blue copper models in the protein

    Ulf Ryde;Mats H. M. Olsson

  • How to obtain statistically converged MM/GBSA results.

    Samuel Genheden;Ulf Ryde

  • Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

    Carl Diehl;Olof Engström;Tamara Delaine;Maria Håkansson

  • On the role of the axial ligand in heme proteins: a theoretical study

    Patrik Rydberg;Emma Sigfridsson;Ulf Ryde

  • The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations

    Ulf Ryde

  • On the Convergence of QM/MM Energies.

    LiHong Hu;Pär Söderhjelm;Ulf Ryde

  • How O2 binds to heme: Reasons for rapid binding and spin inversion

    Kasper P. Jensen;Ulf Ryde

  • The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

    Samuel Genheden;Oliver Kuhn;Paulius Mikulskis;Daniel Hoffmann

  • Theoretical Prediction of the Co−C Bond Strength in Cobalamins

    Kasper P. Jensen;Ulf Ryde

  • Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.

    Hans-Petter Hersleth;Ulf Ryde;Patrik Rydberg;Carl Henrik Görbitz

  • The cupric geometry of blue copper proteins is not strained.

    Ulf Ryde;Mats H.M. Olsson;Kristine Pierloot;Björn O. Roos

  • The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics

    Kadhirvel Saraboji;Maria Håkansson;Samuel Genheden;Carl Diehl

  • A fundamental view of enthalpy–entropy compensation

    Ulf Ryde

  • Relation between the Structure and Spectroscopic Properties of Blue Copper Proteins

    Kristine Pierloot;Jan O A De Kerpel;Ulf Ryde;Mats H M Olsson

  • Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion.

    Ulf Ryde

Frequent Co-Authors

Lubomír Rulíšek
Lubomír Rulíšek Czech Academy of Sciences
Mats Olsson
Mats Olsson University of Gothenburg
Jacob Kongsted
Jacob Kongsted University of Southern Denmark
Luca De Gioia
Luca De Gioia University of Milano-Bicocca
Mikael Akke
Mikael Akke Lund University
Hakon Leffler
Hakon Leffler Lund University
Ulf J. Nilsson
Ulf J. Nilsson Lund University
Björn O. Roos
Björn O. Roos Lund University
Piercarlo Fantucci
Piercarlo Fantucci University of Milano-Bicocca

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