Protein Structures and Complexes: What they Reveal about the Interactions that Stabilize them (original) (raw)
An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
David Baker
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Atomic Environment Energies in Proteins Defined from Statistics of Accessible and Contact Surface Areas
Marc Delarue, Patrice Koehl
Journal of Molecular Biology, 1995
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Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins
Karel Berka
Journal of Chemical Theory and Computation, 2010
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Assessing protein structures with a non-local atomic interaction energy
Francisco Assis Dutra Melo
Journal of Molecular Biology, 1998
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Structure-derived potentials and protein simulations
Robert Jernigan
Current Opinion in Structural Biology, 1996
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A simple physical model for binding energy hot spots in protein–protein complexes
David Baker
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Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations
Yaoqi Zhou
Biochemistry, 2009
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An improved hydrogen bond potential: impact on medium resolution protein structures
Fabiola Fratini
Protein science : a publication of the Protein Society, 2002
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Empirical potentials and functions for protein folding and binding
Sandor Vajda
Current Opinion in Structural Biology, 1997
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An effective all-atom potential for proteins
Sandipan Mohanty
2009
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Determination of atomic desolvation energies from the structures of crystallized proteins
James Cornette
Journal of Molecular Biology, 1997
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Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures
Karel Berka
Journal of Chemical Theory and Computation, 2009
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Protein-Ligand Interactions: Energetic Contributions and Shape Complementarity
Raquel Norel
Encyclopedia of Life Sciences, 2001
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Do we see what we should see? Describing non-covalent interactions in protein structures including precision
Kanagaraj Sekar
IUCrJ, 2013
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Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water
andrea mozzarelli
Journal of Medicinal Chemistry, 2002
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Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interactions
Ioannis (Yannis) P Androulakis
Computers & Chemical Engineering, 1998
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Potential energy stabilizing a hydrophobic core of protein and its contribution to overall stability
Boris Fackovec
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A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
Chi Zhang
Proteins-structure Function and Bioinformatics, 2004
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Protein structure prediction: Do hydrogen bonding and water-mediated interactions suffice?
Chenghang Zong
Methods, 2010
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Helmholtz free energies of atom pair interactions in proteins
Peter Lackner
Folding & design, 1996
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Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations.
David Baker
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Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
Robert Jernigan
Macromolecules, 1985
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Consistency in structural energetics of protein folding and peptide recognition
James Cornette
Protein Science, 1997
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On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures
Javier Garcia
Bioinformatics, 2017
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Hydrophobic regions on protein surfaces. Derivation of the solvation energy from their area distribution in crystallographic protein structures
Frank Eisenhaber
Protein Science, 1996
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Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
André Juffer
Protein Science, 1995
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A structural perspective on protein–protein interactions
Dmitry Korkin
Current Opinion in Structural Biology, 2004
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Identification of a pattern in protein structure based on energetic and statistical considerations
Andrea Amadei
Proteins: Structure, Function, and Genetics, 1996
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
Ngo My
Journal of Physical Chemistry B, 1998
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Determination of interaction potentials of amino acids from native protein structures: Tests on simple lattice models
Flavio Seno
The Journal of Chemical Physics, 1999
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