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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