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Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique

Data up to Jan 2025

Published2002
Citations20
References66

Total Citations Per Year

Abstract

References (66)

Optimization by Simulated Annealing

1983 • 42,775 citations

Classical Electrodynamics

2020 • 23,276 citations

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

1983 • 14,615 citations

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

1998 • 13,827 citations

Molecular Cell Biology

1986 • 5,808 citations

Semianalytical treatment of solvation for molecular mechanics and dynamics

1990 • 3,585 citations

Volumen und Hydratationswärme der Ionen

1920 • 2,234 citations

Modeling of loops in protein structures

2000 • 2,081 citations

Molecular tinkering of G protein-coupled receptors: an evolutionary success

1999 • 1,479 citations

The 2.0 Å crystal structure of a heterotrimeric G protein

1996 • 1,118 citations

How does a protein fold?

1994 • 947 citations

Protein Folding: A Perspective from Theory and Experiment

1998 • 840 citations

Structural basis of substrate specificity in the serine proteases

1995 • 802 citations

The 2.2 Å crystal structure of transducin-α complexed with GTPγS

1993 • 788 citations

Crystal structure of a GA protein βγdimer at 2.1 Å resolution

1996 • 741 citations

Optimized δ expansion for relativistic nuclear models

1998 • 652 citations

Structural determinants for activation of the α-subunit of a heterotrimeric G protein

1994 • 636 citations

On the Theory of Dielectric Polarization

1936 • 517 citations

"New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations

1997 • 514 citations

Prediction of the folding of short polypeptide segments by uniform conformational sampling

1987 • 428 citations

Protein-DNA interactions: a structural analysis

1999 • 425 citations

Ring Closure and Local Conformational Deformations of Chain Molecules

1970 • 410 citations

Gi2 mediates alpha 2-adrenergic inhibition of adenylyl cyclase in platelet membranes: in situ identification with G alpha C-terminal antibodies.

1989 • 374 citations

New Monte Carlo algorithms for protein folding

1999 • 286 citations

Identification of receptor contact site involved in receptor–G protein coupling

1987 • 249 citations

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model

1998 • 243 citations

Mechanisms of Antibody Binding to a Protein

1987 • 210 citations

The Predicted Structure of Immunoglobulin D1.3 and Its Comparison with the Crystal Structure

1986 • 206 citations

Reduction potentials of various aromatic hydrocarbons and their univalent anions

1956 • 203 citations

Folding thermodynamics of a model three-helix-bundle protein

1997 • 165 citations

PDB-based protein loop prediction: parameters for selection and methods for optimization

1997 • 161 citations

Efficient monte carlo method for simulation of fluctuating conformations of native proteins

1985 • 145 citations

Electrostatic effects in water-accessible regions of proteins

1984 • 131 citations

Engineering metal-binding sites in proteins

1997 • 117 citations

A General Treatment of Solvent Effects Based on Screened Coulomb Potentials

2000 • 109 citations

Functional Significance of Loops in The Receptor Binding Domain ofBacillus thuringiensisCryIIIA δ-Endotoxin

1996 • 108 citations

Exact analytical loop closure in proteins using polynomial equations

1999 • 105 citations

Prediction of loop geometries using a generalized born model of solvation effects

1999 • 104 citations

Conformational Memories and the Exploration of Biologically Relevant Peptide Conformations: An Illustration for the Gonadotropin-Releasing Hormone

1996 • 102 citations

Lattice representations of globular proteins: How good are they?

1993 • 98 citations

Signal transduction enzymes of vertebrate photoreceptors

1992 • 89 citations

First-Principle Determination of Peptide Conformations in Solvents: Combination of Monte Carlo Simulated Annealing and RISM Theory

1998 • 82 citations

Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling

1997 • 81 citations

Assessment of comparative modeling in CASP2

1997 • 79 citations

Interactions of a G-protein with its effector: transducin and cGMP phosphodiesterase in retinal rods

1993 • 78 citations

Assessment of comparative modeling in CASP2

1997 • 73 citations

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water 1 1Edited by G. von Heijne

1997 • 70 citations

Simulated Annealing of Chemical Potential: A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA

1996 • 65 citations

Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins

1992 • 63 citations

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

1995 • 59 citations

Free energy landscapes of peptides by enhanced conformational sampling 1 1Edited by B. Honig

2000 • 59 citations

Co-Expression of Lens Fiber Connexins Modifies Hemi-Gap-Junctional Channel Behavior

1999 • 58 citations

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

1994 • 51 citations

Characterization of Hydrogen Bonding in a Continuum Solvent Model

2000 • 50 citations

Protein loops on structurally similar scaffolds: Database and conformational analysis

1999 • 36 citations

Conformational memories and a simulated annealing program that learns: Application to LTB4

1995 • 36 citations

A general screened Coulomb potential based implicit solvent model: Calculation of secondary structure of small peptides

2001 • 33 citations

Loop problem in proteins: Developments on Monte Carlo simulated annealing approach

1996 • 26 citations

Computer Simulations of De Novo Designed Helical Proteins

1998 • 24 citations

Efficiency of simulated annealing for peptides with increasing geometrical restrictions

1999 • 23 citations

Explicit and implicit water simulations of a ?-hairpin peptide

1999 • 22 citations

Predicting immunoglobulin-like hypervariable loops

1994 • 21 citations

Backbone entropy of loops as a measure of their flexibility: Application to a Ras protein simulated by molecular dynamics

1997 • 17 citations

Collective-variable Monte Carlo simulation of DNA

1997 • 14 citations

β-sheet formation in BPTI(16–36) by Monte Carlo simulated annealing

1999 • 13 citations

Simulations of the thermodynamic properties of a short polyalanine peptide using potentials of mean force

1997 • 9 citations

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Structure Calculation of Protein Segments Connecting Domains with Defined Secondary… (2002) – Lecture notes in computational science and engineering | Metascience Observatory Explorer