Evaluation of homology modeling of HIV Protease

Weber, Irene T.

doi:10.1002/prot.340070206

Cited by 57 publications

(23 citation statements)

References 36 publications

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“…In general, the methods employed here in developing the mutant models based on experimentally determined structures have shown a remarkable reproducibility with other proteins, such as HIV protease [28], and have been found to be consistent with X-ray crystallographic results. and its peptides obtained by its digestion with TPCK-trypsin or degradation with oxalic acid, and subsequently analyzed by mass spectrometry.…”

Section: Computer Modeling Of Echistatand Erandtostatin and Echisd27wsupporting

confidence: 64%

Importance of the structure of the RGD‐containing loop in the disintegrins echistatin and eristostatin for recognition of αIIbβ3 and αvβ3 integrins

et al. 1996

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Section: Computer Modeling Of Echistatand Erandtostatin and Echisd27wsupporting

confidence: 64%

Importance of the structure of the RGD‐containing loop in the disintegrins echistatin and eristostatin for recognition of αIIbβ3 and αvβ3 integrins

et al. 1996

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“…A very large number of homology models have been built over the years. Targets have included antibodies[119] and many proteins involved in human biology and medicine[120121]. …”

Section: Applications Of Homology Modelingmentioning

confidence: 99%

Homology modeling a fast tool for drug discovery: Current perspectives

Vk¹,

Ukawala²,

Ghate³

et al. 2012

Indian J Pharm Sci

225

116

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Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.

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“…Understanding the mechanism of protein function generally requires knowledge of protein three-dimensional structure [1][2], which is ultimately determined by protein sequence [3]. Protein structure determination using experimental methods such as X-ray crystallography or NMR spectroscopy is time consuming and not successful with all proteins, especially membrane proteins [4].…”

Section: Introductionmentioning

confidence: 99%

Advances in Homology Protein Structure Modeling

Xiang

2006

CPPS

427

243

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Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the overwhelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function.

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Evaluation of homology modeling of HIV Protease

Cited by 57 publications

References 36 publications

Importance of the structure of the RGD‐containing loop in the disintegrins echistatin and eristostatin for recognition of αIIbβ3 and αvβ3 integrins

Importance of the structure of the RGD‐containing loop in the disintegrins echistatin and eristostatin for recognition of αIIbβ3 and αvβ3 integrins

Homology modeling a fast tool for drug discovery: Current perspectives

Advances in Homology Protein Structure Modeling

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