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Journal of Computational Chemistry

Journal
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Overview

articles

  • Molecular dynamics analysis of Mg2+ -dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis 2020
  • AutoGridFR: Improvements on AutoDock affinity maps and associated software tools 2019
  • "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.  38:1321-1331. 2017
  • Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation.  38:1438-1446. 2017
  • Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation.  38:1229-1237. 2017
  • Molecular simulations to delineate functional conformational transitions in the HCV polymerase.  38:1125-1137. 2017
  • Optimal allosteric stabilization sites using contact stabilization analysis.  38:1138-1146. 2017
  • Residue-centric modeling and design of saccharide and glycoconjugate structures.  38:276-287. 2017
  • Model parameters for simulation of physiological lipids.  37:1112-1118. 2016
  • Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.  35:360-370. 2014
  • Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery.  33:1880-1891. 2012
  • Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions.  32:1431-1440. 2011
  • CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.  31:671-690. 2010
  • AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.  31:455-461. 2010
  • AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility.  30:2785-2791. 2009
  • Additive empirical force field for hexopyranose monosaccharides.  29:2543-2564. 2008
  • Empirical entropic contributions in computational docking: evaluation in APS reductase complexes.  29:1753-1761. 2008
  • Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface.  28:1883-1892. 2007
  • A semiempirical free energy force field with charge-based desolvation.  28:1145-1152. 2007
  • DFT calculations of 57Fe Mossbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media: applications to methane monooxygenase and ribonucleotide reductase.  27:1292-1306. 2006
  • Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.  25:1005-1014. 2004
  • Detailed analysis of grid-based molecular docking: a case study of CDOCKER - A CHARMm-based MD docking algorithm.  24:1549-1562. 2003
  • Icff: A new method to incorporate implicit flexibility into an internal coordinate force field.  24:254-265. 2003
  • Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole.  24:98-110. 2003
  • Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.  23:214-221. 2002
  • Identifying native-like protein structures using physics-based potentials.  23:147-160. 2002
  • Assessing energy functions for flexible docking.  19:1612-1622. 1998
  • Assessing search strategies for flexible docking.  19:1623-1631. 1998
  • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function.  19:1639-1662. 1998
  • Garant - a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra.  18:139-149. 1997
  • Lattice modeling: accuracy of energy calculations.  17:1025-1032. 1996
  • The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization.  8:132-141. 1987
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Identity

International Standard Serial Number (ISSN)

  • 0192-8651

Electronic International Standard Serial Number (EISSN)

  • 1096-987X

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