(Q30009563)

21 May 2017

title

Computational protein design: the Proteus software and selected applications (English)

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21 May 2017

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computational biology

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Thomas Gaillard

2

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Thomas Simonson

object named as

Thomas Simonson

1

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author name string

David Mignon

3

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21 May 2017

Marcel Schmidt am Busch

4

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21 May 2017

Anne Lopes

5

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21 May 2017

Najette Amara

6

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21 May 2017

Savvas Polydorides

7

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21 May 2017

Audrey Sedano

8

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21 May 2017

Karen Druart

9

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21 May 2017

Georgios Archontis

10

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21 May 2017

language of work or name

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26 August 2013

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Journal of Computational Chemistry

21 May 2017

published in

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21 May 2017

volume

34

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21 May 2017

issue

28

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21 May 2017

page(s)

2472-2484

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Prediction and design of macromolecular structures and interactions

21 May 2017

cites work

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Computer-based design of novel protein structures

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Progress in computational protein design

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Protein design in metabolic engineering and synthetic biology

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Recent advances in computational protein design.

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Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins

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Theoretical and computational protein design

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Computational design of receptor and sensor proteins with novel functions

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Automated design of specificity in molecular recognition

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Enzyme-like proteins by computational design

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A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins

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Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

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De novo design of a beta alpha beta motif

21 January 2018

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Principles for designing ideal protein structures

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Kemp elimination catalysts by computational enzyme design

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De novo computational design of retro-aldol enzymes

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De novo enzyme design using Rosetta3

21 January 2018

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Computational protein design: Advances in the design and redesign of biomolecular nanostructures

21 January 2018

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Exploring Symmetry as an Avenue to the Computational Design of Large Protein Domains

21 January 2018

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Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

21 January 2018

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Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

21 January 2018

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Computational design of a protein crystal

21 January 2018

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

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Force fields for protein simulations

21 January 2018

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Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

21 January 2018

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CHARMM: the biomolecular simulation program

21 January 2018

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Atomic-Level Characterization of the Structural Dynamics of Proteins

21 January 2018

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Computations of standard binding free energies with molecular dynamics simulations

21 January 2018

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Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

21 January 2018

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Free energy simulations come of age: protein-ligand recognition

21 January 2018

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21 January 2018

Implicit solvent models

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Recent advances in the development and application of implicit solvent models in biomolecule simulations

21 January 2018

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An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design

21 January 2018

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Effective scoring function for protein sequence design.

21 January 2018

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Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

21 January 2018

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An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

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Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity.

21 January 2018

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Optimal sequence selection in proteins of known structure by simulated evolution

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An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants

21 January 2018

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De novo protein design. I. In search of stability and specificity.

21 January 2018

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Designing proteins from the inside out.

21 January 2018

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An object-oriented library for computational protein design.

21 January 2018

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Computational design of antibody-affinity improvement beyond in vivo maturation

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Folding free energy function selects native-like protein sequences in the core but not on the surface

21 January 2018

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Challenges in the computational design of proteins

21 January 2018

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OSPREY: protein design with ensembles, flexibility, and provable algorithms

21 January 2018

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Computational protein design: software implementation, parameter optimization, and performance of a simple model.

21 January 2018

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Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

21 January 2018

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De novo protein design: fully automated sequence selection

21 January 2018

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Generalized born models of macromolecular solvation effects

21 January 2018

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Computational sidechain placement and protein mutagenesis with implicit solvent models.

21 January 2018

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Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

21 January 2018

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Backbone flexibility in computational protein design

21 January 2018

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RosettaRemodel: a generalized framework for flexible backbone protein design.

21 January 2018

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Computational protein design as a tool for fold recognition

21 January 2018

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Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition

21 January 2018

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The SUPERFAMILY database in 2007: families and functions

21 January 2018

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Computational protein design with a generalized Born solvent model: application to Asparaginyl-tRNA synthetase.

21 January 2018

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Very fast empirical prediction and rationalization of protein pKa values

21 January 2018

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Improved prediction of protein side-chain conformations with SCWRL4

21 January 2018

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Pairwise calculation of protein solvent-accessible surface areas

21 January 2018

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A surprising simplicity to protein folding.

21 January 2018

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CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

21 January 2018

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Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation

21 January 2018

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A residue-pairwise generalized born scheme suitable for protein design calculations.

21 January 2018

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Accurate, conformation-dependent predictions of solvent effects on protein ionization constants

21 January 2018

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The interpretation of protein structures: Estimation of static accessibility

21 January 2018

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Automatic protein design with all atom force-fields by exact and heuristic optimization

21 January 2018

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Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

21 January 2018

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Statistical theory for protein ensembles with designed energy landscapes

21 January 2018

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Equation of State Calculations by Fast Computing Machines

21 January 2018

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Constant pH molecular dynamics in generalized Born implicit solvent

21 January 2018

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Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

21 January 2018

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Protein design automation

21 January 2018

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A Novel View of pH Titration in Biomolecules†

21 January 2018

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Expanding the genetic code of Escherichia coli

21 January 2018

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Beyond the canonical 20 amino acids: expanding the genetic lexicon

21 January 2018

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Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine

21 January 2018

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Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms

21 January 2018

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A new approach to the rapid determination of protein side chain conformations

21 January 2018

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Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

21 January 2018

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Progress in the prediction of pKa values in proteins

21 January 2018

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Protein modules and signalling networks

21 January 2018

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Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk

21 January 2018

1 reference

Pfam: clans, web tools and services

21 January 2018

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SCOP database in 2004: refinements integrate structure and sequence family data

21 January 2018

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

21 January 2018

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Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

21 January 2018

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Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease

21 January 2018

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Very fast prediction and rationalization of pKa values for protein-ligand complexes

21 January 2018

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Rapid calculation of protein pKa values using Rosetta

21 January 2018

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MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

21 January 2018

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Poisson–Boltzmann Methods for Biomolecular Electrostatics

21 January 2018

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Protein molecular dynamics with the generalized born/ACE solvent model

21 January 2018

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Pairwise solute descreening of solute charges from a dielectric medium

21 January 2018

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PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.23418

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journals/jcc/SimonsonGMBLAPSDA13

21 May 2017

DBLP publication ID

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DBLP Dataset 2021-01-02

28 January 2021

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