Modeling side-chain conformation (Q28285711)

Current Opinion in Structural Biology

Europe PubMed Central

title

Modeling side-chain conformation (English)

0 references

author name string

M Vásquez

series ordinal

1

0 references

language of work or name

English

0 references

publication date

April 1996

0 references

published in

0 references

volume

6

0 references

issue

2

0 references

page(s)

217-21

0 references

cites work

Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

An analysis of packing in the protein folding problem

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Core-packing constraints, hydrophobicity and protein design

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Conformation of amino acid side-chains in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

A statistical analysis of side-chain conformations in proteins: comparison with ECEPP predictions

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Determinants of protein side-chain packing

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Prediction of protein side-chain conformation by packing optimization.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Predicting protein mutant energetics by self-consistent ensemble optimization.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Modeling side-chain conformation for homologous proteins using an energy-based rotamer search

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Homology modelling of annexin I: implicit solvation improves side-chain prediction and combination of evaluation criteria allows recognition of different types of conformational error

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

A method to configure protein side-chains from the main-chain trace in homology modelling

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Prediction of protein side-chain conformations from local three-dimensional homology relationships

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

The crystal structure of a mutant protein with altered but improved hydrophobic core packing

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

The dead-end elimination theorem and its use in protein side-chain positioning

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Efficient rotamer elimination applied to protein side-chains and related spin glasses

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side chains

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Finding the global minimum: a fuzzy end elimination implementation

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Equation of State Calculations by Fast Computing Machines

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Optimization by Simulated Annealing

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Side-chain prediction by neural networks and simulated annealing optimization.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Optimal sequence selection in proteins of known structure by simulated evolution

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Ligand docking to proteins with discrete side-chain flexibility.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Prediction of homologous protein structures based on conformational searches and energetics.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

9 Modeling of side chains, loops, and insertions in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Repacking protein cores with backbone freedom: structure prediction for coiled coils

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Multiple copy sampling: rigid versus flexible protein.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

Local moves: an efficient algorithm for simulation of protein folding.

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021

A general model of invariant chain association with class II major histocompatibility complex proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0959-440X%2896%2980077-7

7 January 2021