Expanding molecular modeling and design tools to non-natural sidechains (Q43745380)

26 November 2017

Expanding molecular modeling and design tools to non-natural sidechains (English)

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26 November 2017

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26 November 2017

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Olivier Michielin

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26 November 2017

Vincent Zoete

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26 November 2017

14 April 2012

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Journal of Computational Chemistry

26 November 2017

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26 November 2017

33

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26 November 2017

18

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26 November 2017

1525-1535

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Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

26 November 2017

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Assembly of Cell Regulatory Systems Through Protein Interaction Domains

21 January 2018

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Large-scale structural analysis of the classical human protein tyrosine phosphatome

21 January 2018

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Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides

21 January 2018

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Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

21 January 2018

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Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target

21 January 2018

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The multiple-specificity landscape of modular peptide recognition domains

21 January 2018

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Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

21 January 2018

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A chemical toolkit for proteins--an expanded genetic code

21 January 2018

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A phage display system with unnatural amino acids

21 January 2018

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A highly flexible tRNA acylation method for non-natural polypeptide synthesis.

21 January 2018

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Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

21 January 2018

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The FoldX web server: an online force field

21 January 2018

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Protein-protein docking with backbone flexibility.

21 January 2018

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GROMACS: fast, flexible, and free

21 January 2018

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CHARMM: the biomolecular simulation program

21 January 2018

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ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

21 January 2018

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SwissParam: A fast force field generation tool for small organic molecules

21 January 2018

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UCSF Chimera--a visualization system for exploratory research and analysis

21 January 2018

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Rotamer libraries in the 21st century

21 January 2018

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Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes

21 January 2018

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Improved prediction of protein side-chain conformations with SCWRL4

21 January 2018

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Bayesian statistical analysis of protein side-chain rotamer preferences

21 January 2018

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A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

21 January 2018

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Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.

21 January 2018

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Using quantum mechanics to improve estimates of amino acid side chain rotamer energies

21 January 2018

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NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids

21 January 2018

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FACTS: Fast analytical continuum treatment of solvation.

21 January 2018

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New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

21 January 2018

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Analysis of the interaction of BCL9 with beta-catenin and development of fluorescence polarization and surface plasmon resonance binding assays for this interaction.

21 January 2018

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Crystal structure of a beta-catenin/BCL9/Tcf4 complex

21 January 2018

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Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.

21 January 2018

1 reference

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

21 January 2018

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Design of cyclic peptides that bind protein surfaces with antibody-like affinity

21 January 2018

1 reference

Phage-encoded combinatorial chemical libraries based on bicyclic peptides

21 January 2018

1 reference

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

21 January 2018

1 reference

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/JCC.22982

1 reference

26 November 2017

journals/jcc/GfellerMZ12

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DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

22505320