Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interactions (original) (raw)

Determination of the Stable Microstates of a Peptide from NOE Distance Constraints and Optimization of Atomic Solvation Parameters

Canan Atilgan

Journal of the American Chemical Society, 1998

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Evaluation of the dipeptide approximation in peptide modeling by ab initio geometry optimizations of oligopeptides

Anik Peeters

Journal of the American Chemical Society, 1993

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Calculation of protein conformation by global optimization of a potential energy function

Adam Liwo

Proteins-structure Function and Bioinformatics, 1999

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PEPCONF, a diverse data set of peptide conformational energies

Viki Prasad

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Solvation Energy of Biomolecular Structures: A Study of the Effect of Salt on Biomolecules Through Implicit as Well as Explicit Solvation Methods

Mihir Date

2012

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Solvent effects on conformational stability of peptides: RISM analyses

Fumio Hirata

Journal of Molecular Liquids, 2001

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Use of genetic algorithms and solvation potential to study peptides structure

Jose Ruggiero

Applied Mathematics and Computation, 2008

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New insights into the multiple minima problem associated with the conformational space of peptides

Nuria Centeno

Chemical Physics Letters, 1995

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Exploring Peptide–Solvent Interactions: A Computational Study

Nadia Elghobashi-Meinhardt

Molecules, 2018

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Recent improvements in prediction of protein structure by global optimization of a potential energy function

Adam Liwo

Proceedings of The National Academy of Sciences, 2001

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Free energies of solvation for peptides and polypeptides using SCRF methods

Hamilton Ishiki

Chemical Physics, 1998

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Determining minimum energy conformations of polypeptides by dynamic programming

Sandor Vajda

Biopolymers, 1990

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Evaluation of the iterative simulated annealing technique in conformational search of peptides

Francesc Corcho

Chemical Physics Letters, 2000

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Predicting peptides structure with solvation potential and rotamer library dependent of the backbone

Jose Ruggiero

Applied Mathematics and Computation, 2008

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Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides

Bun Chan

Australian Journal of Chemistry, 2018

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Structural and Dynamic Properties of a .beta.-Hairpin-Forming Linear Peptide. 1. Modeling Using Ensemble-Averaged Constraints

Robert Bruccoleri

Journal of the American Chemical Society, 1995

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Computational Study of the Conformational Domains of Peptide T

Nuria Centeno

Journal of Peptide Science, 1997

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Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling

William Goddard

Protein Science, 1995

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Molecular dynamics simulation and conformational analysis of some catalytically active peptides

Bahareh Honarparvar, Adam Skelton

Journal of Molecular Modeling, 2015

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New optimization method for conformational energy calculations on polypeptides: Conformational space annealing

S. Rackovsky

Journal of Computational Chemistry, 1997

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The solvation interface is a determining factor in peptide conformational preferences

Vijay Pande

2006

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Searching Peptide Conformational Space

Frank Jensen

Journal of Chemical Theory and Computation, 2011

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Conditional Solvation Thermodynamics of Isoleucine in Model Peptides and the Limitations of the Group-Transfer Model

Dheeraj singh tomar

The Journal of Physical Chemistry B, 2014

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Modeling of the Amino Acid Side Chain Effects on Peptide Conformation

Mati Karelson

Bioorganic Chemistry, 1999

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Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces

Roger Beuerman, Dilraj Lama, Christopher Brown

Scientific reports, 2013

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Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model

Juan Almagro

Proteins: Structure, Function, and Genetics, 1998

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Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics B

Milena Guida

The Journal of Physical Chemistry, 2015

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Protein Structure Prediction by Global Optimization of a Potential Energy Function

Adam Liwo

Proceedings of The National Academy of Sciences, 1999

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Investigation of Noncovalent Interactions in Deprotonated Peptides: Structural and Energetic Competition between Aggregation and Hydration

Thomas Wyttenbach

Journal of the American Chemical Society, 2004

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A semi-implicit solvent model for the simulation of peptides and proteins

Daniel Borgis

Journal of Computational Chemistry, 2004

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A Mathematical Model for Analytical Fitting of Amino Acid Diamide Conformational Potential Energy Surfaces

Adrian Roy Valdez

International Journal of Chemical Engineering and Applications

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Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

Sandor Vajda

Biochemistry, 1994

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