Cited by 295Protein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods

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Progress in Modeling of Protein Structures and Interactions.

Schueler-Furman, Ora, Wang, Chu, Bradley, Phil, Misura, Kira, Baker, David·2005·Science

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Abstract

The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.

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Direct correlation between proteins' folding rates and their amino acid compositions: An ab initio folding rate prediction
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What is the biological relevance of the specific bond properties revealed by single‐molecule studies?
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Backbone Flexibility Controls the Activity and Specificity of a Protein−Protein Interface: Specificity in Snake Venom Metalloproteases
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Generalized ensemble methods for de novo structure prediction
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“For this reason, there are multiscale approaches that start with low-resolution or reduced-model energy functions and then use all-atom energy functions on a few selected conformations [often relying on additional steps such as use of sequence homologs (2) or clustering (3, 4)] been developed (4, 6, 12, 13).”
Background
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Structure‐guided forcefield optimization
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Self-citation
Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface
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“Nevertheless, the accuracy of current energetic functions [7,12,13,14,15,16,17] has been a formidable barrier [18].”
Background
The Outer-Coordination Sphere: Incorporating Amino Acids and Peptides as Ligands for Homogeneous Catalysts to Mimic Enzyme Function
Shaw, W. J. (2012) · Catalysis Reviews · doi:10.1080/01614940.2012.679453 · Cited by 48
Protein folding prediction in 3D FCC HP lattice model using genetic algorithm
Hoque, M. T., Chetty, M., & Sattar, A. (2007) · IEEE Congress on Evolutionary Computation (CEC) · doi:10.1109/cec.2007.4425011 · Cited by 47
A Guide to Template Based Structure Prediction
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Quantum Chemistry Simulation of Biological Molecules
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Extended HP Model for Protein Structure Prediction
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“The usefulness of the low-resolution modeling for solving the ab initio PSP problem in practice can be found elsewhere (Baker, 2006; Chivian et al., 2003; Samudrala et al., 1999; Hinds and Levitt, 1994; Koehl and Levitt, 1999; Kolinski et al., 2003; Schueler-Furman et al., 2005; Xia et al., 2000).”
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
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“Background Reliable high-resolution prediction of protein structure remains a formidable challenge and it becomes more and more evident that we are entering the era in which highresolution predictions and molecular designs will make increasingly important contributions to biology and medicine [1,2].”
Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides
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Authors: Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., & Baker, D.
Affiliations: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Howard Hughes Medical Institute (US)
Corresponding author: Baker, David
ORCID: Wang, Chu
Baker, David
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2005-10-28
Volume: 310
Issue: 5748
Pages: 638-642
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.1112160
OpenAlex: W2147752484
Cited by: 294
References: 65
Citations by year: 2025: 4 · 2024: 4 · 2023: 2 · 2022: 2 · 2021: 4 · 2020: 5 · 2019: 8 · 2018: 2 · 2017: 8 · 2016: 9 · 2015: 9 · 2014: 8 · 2013: 10 · 2012: 16
FWCI: 3.31
Type: journal article
Language: en
Open access: closed
Locations: Science (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Keywords: protein structure prediction, protein-protein interaction, interatomic interactions, genome interpretation
MeSH terms: Computer Simulation, Computing Methodologies, Models, Molecular, Protein Conformation

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