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Molecular design software

Molecular design software is software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to… 
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AbaloneAscalaph DesignerAssisted Model Building with Energy Refinement (AMBER)Avogadro

Papers overview

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2015
2015
The design of two proteins that have 100% sequence identity but encode different folds
Title of Document: THE DESIGN OF TWO PROTEINS THAT HAVE 100% SEQUENCE IDENTITY BUT ENCODE DIFFERENT FOLDS Dana Motabar, Master of… 
Review
2014
Review
2014
A Critical Review of Computational Protein Design Strategies : Progress , Limitations , and Improvements
The question of how a protein’s 3D structure is encoded by its amino acid sequence, and how that structure in turn dictates its… 
2010
2010
Methods and applications in computational protein design
In this thesis, we summarize our work on applications and methods for computational protein design. First, we apply computational… 
2008
2008
Using Protein Design to Understand the Role of Electrostatic Interactions on Calcium Binding Affinity and Molecular Recognition
Calcium regulates many biological processes through interaction with proteins with different conformational, dynamic, and metal… 
2008
2008
Accurate Prediction for Atomic-Level Protein Design Implies High Similarity in the Near-Optimal Sequence Space
The task of engineering a protein to assume a target three-dimensional structure is known as protein design. Computational search… 
2007
2007
DNA sequence selectivity and kinetic properties of de novo designed metalloprotein dimers
In our efforts to engineer a DNA binding and cleaving protein with greater sequence discrimination, we have designed dimeric… 
2007
2007
Protein Design by Mining and Sampling an Undirected Graphical Protein Design by Mining and Sampling an Undirected Graphical Model of Evolutionary Constraints Model of Evolutionary Constraints
Evolutionary pressures on proteins to maintain structure and function have constrained their sequences over time and across… 
2004
2004
Handel continuum electrostatics and solvation Energy functions for protein design I : Efficient and accurate data
Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular… 
1998
1998
Secondary structure formation in beta-Peptides
A very actual subject of research in the field of peptide an protein design are oligomers of β-amino acids called β-peptides… 
1989
1989
Advances in protein design, international workshop 1988
Part 1: Methods and theoretical concepts: thermodynamic and kinetic aspects of the folding and self-assembly of proteins folding…