Molecular docking using surface complementarity

Sobolev, V. M.; Wade, Rebecca C.; Vriend, Gert; Edelman, Marvin

doi:10.1002/(sici)1097-0134(199605)25:1<120::aid-prot10>3.0.co;2-m

Cited by 98 publications

(8 citation statements)

References 58 publications

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“…Another possibility is to identify hydrophobic clusters directly in a protein structure. Their computation is based on the Contacts of Structural Units (CSU) algorithm, which is also widely used to calculate contact maps ( 22 , 29 ). Although the CSU algorithm was initially released as a package and web server, both are unfortunately no longer available.…”

Section: Methodsmentioning

confidence: 99%

ProteinTools: a toolkit to analyze protein structures

Ferruz

Schmidt

Höcker

2021

Nucleic Acids Research

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The experimental characterization and computational prediction of protein structures has become increasingly rapid and precise. However, the analysis of protein structures often requires researchers to use several software packages or web servers, which complicates matters. To provide long-established structural analyses in a modern, easy-to-use interface, we implemented ProteinTools, a web server toolkit for protein structure analysis. ProteinTools gathers four applications so far, namely the identification of hydrophobic clusters, hydrogen bond networks, salt bridges, and contact maps. In all cases, the input data is a PDB identifier or an uploaded structure, whereas the output is an interactive dynamic web interface. Thanks to the modular nature of ProteinTools, the addition of new applications will become an easy task. Given the current need to have these tools in a single, fast, and interpretable interface, we believe that ProteinTools will become an essential toolkit for the wider protein research community. The web server is available at https://proteintools.uni-bayreuth.de.

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Section: Methodsmentioning

confidence: 99%

ProteinTools: a toolkit to analyze protein structures

Ferruz

Schmidt

Höcker

2021

Nucleic Acids Research

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“…Finally, represent the surface area in contact between atoms and calculated analytically [48] . We utilize the atom types classification of Sobolev et al [76] containing 8 atom types. A matrix with all the interaction between atom types set at the value 1 is used in the non-specific ENCoM ns model.…”

Section: Methodsmentioning

confidence: 99%

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

2014

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Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations.

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“…Attractive interactions are introduced between native contacts when these pairs are in proximity, whereas the rest of the pairs have repulsive interactions. The contacting residue pairs are determined using the Contacts of Structural Units method (43). In a vanilla model, all interactions are equally scored, with no regard to their original chemical nature.…”

Section: Coarse-grained Molecular-dynamics Simulationsmentioning

confidence: 99%

Modulation of Folding Kinetics of Repeat Proteins: Interplay between Intra- and Interdomain Interactions

Hagai

Azia

Trizac

et al. 2012

Biophysical Journal

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Repeat proteins have unique elongated structures that, unlike globular proteins, are quite modular. Despite their simple one-dimensional structure, repeat proteins exhibit intricate folding behavior with a complexity similar to that of globular proteins. Therefore, repeat proteins allow one to quantify fundamental aspects of the biophysics of protein folding. One important feature of repeat proteins is the interfaces between the repeating units. In particular, the distribution of stabilities within and between the repeats was previously suggested to affect their folding characteristics. In this study, we explore how the interface affects folding kinetics and cooperativity by investigating two families of repeat proteins, namely, the Ankyrin and tetratricopeptide repeat proteins, which differ in the number of interfacial contacts that are formed between their units as well as in their folding behavior. By using simple topology-based models, we show that modulating the energetic strength of the interface relative to that of the repeat itself can drastically change the protein stability, folding rate, and cooperativity. By further dissecting the interfacial contacts into several subsets, we isolated the effects of each of these groups on folding kinetics. Our study highlights the importance of interface connectivity in determining the folding behavior.

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Molecular docking using surface complementarity

Cited by 98 publications

References 58 publications

ProteinTools: a toolkit to analyze protein structures

ProteinTools: a toolkit to analyze protein structures

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

Modulation of Folding Kinetics of Repeat Proteins: Interplay between Intra- and Interdomain Interactions

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