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searching for Homology modeling 62 found (118 total)

RAPTOR (software) (1,124 words) [view diff] exact match in snippet view article

reliable model of the protein. Protein threading is more effective than homology modeling, especially for proteins which have few homologs detectable by sequence

Protein engineering (7,426 words) [view diff] exact match in snippet view article find links to article

of the four following classes: ab initio, fragment based methods, homology modeling, and protein threading.[page needed] These methods involve free modeling

Partitiviridae (553 words) [view diff] case mismatch in snippet view article find links to article

Trace of Partitivirus Capsid Protein from Electron Cryomicroscopy and Homology Modeling". Biophysical Journal. 99 (2): 685–694. Bibcode:2010BpJ....99..685T

Jeffrey Skolnick (1,417 words) [view diff] exact match in snippet view article find links to article

important functional consequences. He also pioneered the field of ligand homology modeling with his threading based, FINDSITE approach for protein function inference

MolIDE (147 words) [view diff] exact match in snippet view article find links to article

MolIDE: Computer programs for side-chain conformation prediction and homology modeling". Nature Protocols. 3 (12): 1832–47. doi:10.1038/nprot.2008.184. PMC 2682191

Alkb homolog 1, histone h2a dioxygenase (584 words) [view diff] exact match in snippet view article find links to article

PMID 19959401. Shankaracharya, Das S, Vidyarthi AS (September 2011). "Homology modeling and function prediction of hABH1, involving in repair of alkylation

MMP20 (639 words) [view diff] exact match in snippet view article find links to article

FS (2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

MMP23B (657 words) [view diff] exact match in snippet view article find links to article

FS (2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

Discovery Studio (884 words) [view diff] exact match in snippet view article find links to article

Mechanics Software Molecular Modeling Molecular Design Software Protein homology modeling MDL Chime "BIOVIA". Dassault Systèmes. August 11, 2023. "List of key

UCSF Chimera (759 words) [view diff] exact match in snippet view article find links to article

Clustal Omega and MUSCLE Web services interfaces to MODELLER for homology modeling and loop building structure superposition with or without pre-existing

MMP26 (994 words) [view diff] exact match in snippet view article find links to article

enzyme inhibition kinetic studies, protein sequence analyses, and homology modeling". J. Biol. Chem. 278 (51): 51646–53. doi:10.1074/jbc.M310109200. PMID 14532275

GeNMR (1,139 words) [view diff] exact match in snippet view article find links to article

uses homology modeling and sequence/structure threading to rapidly generate a first-pass model of the query protein. The use of homology modeling/threading

Hypothetical protein (834 words) [view diff] exact match in snippet view article find links to article

Pharmacy Research. 9: 278–287. Dilip Gore Ashish Chakule (2012). "Homology modeling and function prediction in uncharacterized proteins of Pseudoxanthomonas

MMP19 (956 words) [view diff] exact match in snippet view article find links to article

FS (2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

MMP17 (946 words) [view diff] exact match in snippet view article find links to article

FS (2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

MMP15 (945 words) [view diff] exact match in snippet view article find links to article

(June 2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

Tamulotoxin (998 words) [view diff] exact match in snippet view article find links to article

1016/S0165-6147(99)01398-X. PMID 10542442. Kumar, RB; Suresh, MX (10 January 2013). "Homology modeling, molecular dynamics simulation and protein-protein interaction studies

Interleukin-7 receptor (550 words) [view diff] exact match in snippet view article find links to article

8266077. PMID 8266077. Kroemer RT, Richards WG (December 1996). "Homology modeling study of the human interleukin-7 receptor complex". Protein Eng. 9

Vesicular glutamate transporter 3 (548 words) [view diff] exact match in snippet view article find links to article

PMID 18674745. Almqvist J, Huang Y, Laaksonen A, et al. (2007). "Docking and homology modeling explain inhibition of the human vesicular glutamate transporters"

Comparison of software for molecular mechanics modeling (380 words) [view diff] exact match in snippet view article find links to article

QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc

MMP16 (982 words) [view diff] exact match in snippet view article find links to article

FS (2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

Mannose phosphate isomerase (998 words) [view diff] exact match in snippet view article find links to article

"Computational study of human phosphomannose isomerase: Insights from homology modeling and molecular dynamics simulation of enzyme bound substrate". Journal

ABCG2 (1,287 words) [view diff] exact match in snippet view article find links to article

11850/256191. PMID 29610494. S2CID 4617388. Hazai E, Bikádi Z (April 2008). "Homology modeling of breast cancer resistance protein (ABCG2)". Journal of Structural

Matrix metallopeptidase 12 (1,157 words) [view diff] exact match in snippet view article find links to article

FS (2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". J. Biomol

Vesicular glutamate transporter 1 (601 words) [view diff] exact match in snippet view article find links to article

S2CID 3133505. Almqvist J, Huang Y, Laaksonen A, et al. (2007). "Docking and homology modeling explain inhibition of the human vesicular glutamate transporters"

CYP1B1 (1,185 words) [view diff] exact match in snippet view article find links to article

Stoilov I, Akarsu AN, Alozie I, et al. (1998). "Sequence analysis and homology modeling suggest that primary congenital glaucoma on 2p21 results from mutations

Ion channel (5,954 words) [view diff] case mismatch in snippet view article find links to article

Sylte, I. (2011). Homology Modeling of Transporter Proteins (Carriers and Ion Channels). In: Orry, A., Abagyan, R. (eds) Homology Modeling. Methods in Molecular

Protein structure database (756 words) [view diff] exact match in snippet view article find links to article

SWISS-MODEL Repository a database of annotated protein models calculated by homology modeling TOPSAN the Open Protein Structure Annotation Network — a wiki designed

Protein secondary structure (3,150 words) [view diff] exact match in snippet view article find links to article

in the prediction of tertiary structure, in all but the simplest (homology modeling) cases. For example, a confidently predicted pattern of six secondary

Complement component 1s (1,195 words) [view diff] exact match in snippet view article find links to article

protease C1s: study by chemical cross-linking and three-dimensional homology modeling". Biochemistry. 34 (22): 7311–21. doi:10.1021/bi00022a004. PMID 7779774

Chenopodium album (1,789 words) [view diff] exact match in snippet view article find links to article

Varasteh, A. (April 2011). "Chenopodium album pollen profilin (Che a 2): homology modeling and evaluation of cross-reactivity with allergenic profilins based

Hassan Khachfe (236 words) [view diff] exact match in snippet view article find links to article

N-terminal domain of apolipoprotein B-100: structural characterization by homology modeling". BMC Biochemistry. 8 (1): 12. doi:10.1186/1471-2091-8-12. ISSN 1471-2091

Complement component 1r (1,273 words) [view diff] exact match in snippet view article find links to article

C1r: a three-dimensional model based on chemical cross-linking and homology modeling". Biochemistry. 36 (21): 6270–82. doi:10.1021/bi962719i. PMID 9174342

LIAS (gene) (484 words) [view diff] exact match in snippet view article

Hassan S, Hanna LE, Padmalayam I, Rajaram R, Viswanathan V (2017). "Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights

Thromboxane-A synthase (2,231 words) [view diff] exact match in snippet view article find links to article

detergent treatment extraction from the membrane but they have utilized homology modeling to create a 3D structure. One model showed two domains, an alpha-helix-rich

CYP4A11 (2,570 words) [view diff] exact match in snippet view article find links to article

Therapeutics. 285 (3): 1327–36. PMID 9618440. Chang YT, Loew GH (Feb 1999). "Homology modeling and substrate binding study of human CYP4A11 enzyme". Proteins. 34

Matrix metallopeptidase 13 (1,784 words) [view diff] exact match in snippet view article find links to article

(June 2000). "Structural differences of matrix metalloproteinases. Homology modeling and energy minimization of enzyme-substrate complexes". Journal of

Chromodomain (1,268 words) [view diff] exact match in snippet view article find links to article

structural studies, including those utilizing the Protein Data Bank and homology modeling, have facilitated the rational design of such variants. These strategies

Crotamine (1,395 words) [view diff] exact match in snippet view article find links to article

were supported with intensive molecular dynamics simulations and homology modeling procedures. Afterwards, Nicastro et al. (2003) discovered the structure

M. Radhakrishna Pillai (scientist) (1,436 words) [view diff] exact match in snippet view article

S2CID 29106828. Hariharan, Ramkumar; Radhakrishna Pillai, M. (2006). "Homology modeling of the DNA-binding domain of human Smad5: a molecular model for inhibitor

Succinate dehydrogenase (2,997 words) [view diff] exact match in snippet view article find links to article

structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies". The

Ribonomics (437 words) [view diff] exact match in snippet view article find links to article

"T-cell epitopes of the La/SSB autoantigen: prediction based on the homology modeling of HLA-DQ2/DQ7 with the insulin-B peptide/HLA-DQ8 complex". J Comput

Framework region (1,075 words) [view diff] exact match in snippet view article find links to article

(2014-08-01). "Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction". Proteins: Structure

ANGPTL8 (1,527 words) [view diff] exact match in snippet view article find links to article

until now.[when?] However, the structure of ANGPTL8 was predicted by homology modeling and is also reported in literature. It consists of alpha helices and

Complementarity plot (1,364 words) [view diff] exact match in snippet view article find links to article

unbalanced partial charges within protein interiors. It is useful in homology modeling and protein design. A version of the plot (CPint) has also been built

Dopamine agonist (5,014 words) [view diff] exact match in snippet view article find links to article

Platania CB, Salomone S, Leggio GM, Drago F, Bucolo C (2012-09-06). "Homology modeling of dopamine D2 and D3 receptors: molecular dynamics refinement and

Protein–protein interaction prediction (2,915 words) [view diff] exact match in snippet view article find links to article

server to predict interacting protein pairs and interacting sites by homology modeling of complex structures" Nucleic Acids Research, 36 (S2): 185-. Kittichotirat

Enzyme Function Initiative (1,502 words) [view diff] case mismatch in snippet view article find links to article

"Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening". Structure. 16 (11): 1668–77. doi:10.1016/j

Backbone-dependent rotamer library (2,017 words) [view diff] exact match in snippet view article find links to article

side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool". Journal of Molecular Biology. 267 (5): 1268–82. doi:10.1006/jmbi

Chikashi Toyoshima (1,076 words) [view diff] exact match in snippet view article find links to article

S2CID 4316039. Haruo, Ogawa; Chikashi, Toyoshima (10 December 2002). "Homology modeling of the cation binding sites of Na+,K+-ATPase". PNAS. 99 (25): 15977–82

Aspergillus fumigatus (4,593 words) [view diff] exact match in snippet view article find links to article

amino acid changes in Aspergillus fumigatus CYP51A based on protein homology modeling". Antimicrobial Agents and Chemotherapy. 54 (6): 2425–30. doi:10.1128/AAC

Structural alignment software (782 words) [view diff] exact match in snippet view article find links to article

related protein structures: algorithm, bound and implications to homology modeling". Bioinformatics. 27 (18): 2537–45. doi:10.1093/bioinformatics/btr432

Lucy Forrest (780 words) [view diff] case mismatch in snippet view article find links to article

Tang, Christopher L.; Honig, Barry (2006-07-15). "On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins". Biophysical

Multiple sequence alignment (6,213 words) [view diff] exact match in snippet view article find links to article

in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2

G protein-coupled receptor (9,408 words) [view diff] exact match in snippet view article find links to article

provided a scaffold which was hoped to be a universal template for homology modeling and drug design for other GPCRs – a notion that proved to be too optimistic

MSH2 (4,237 words) [view diff] exact match in snippet view article find links to article

Dowen JM, Putnam CD, Kolodner RD (July 2010). "Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending

GABRB2 (5,576 words) [view diff] exact match in snippet view article find links to article

PMID 25194483. Cheng J, Ju XL, Chen XY, Liu GY (September 2009). "Homology modeling of human alpha 1 beta 2 gamma 2 and house fly beta 3 GABA receptor

List of sequence alignment software (2,358 words) [view diff] exact match in snippet view article find links to article

383–384. doi:10.1145/2555243.2555280. Chivian, D; Baker, D (2006). "Homology modeling using parametric alignment ensemble generation with consensus and

Beta-ketoacyl-ACP synthase III (2,909 words) [view diff] exact match in snippet view article find links to article

and a small molecule inhibitor achieved using rational design and homology modeling". J. Med. Chem. 46 (1): 5–8. doi:10.1021/jm025571b. PMID 12502353

Marta Filizola (2,163 words) [view diff] exact match in snippet view article find links to article

PMID 18668123. Mobarec JC, Sanchez R, Filizola M (2009). "Modern homology modeling of G-protein coupled receptors: which structural template to use?"

Edward Trifonov (4,324 words) [view diff] exact match in snippet view article find links to article

through the protein sequence space: Towards new generation of the homology modeling". Proteins: Structure, Function, and Bioinformatics. 67 (2): 271–284

List of RNA structure prediction software (8,490 words) [view diff] exact match in snippet view article find links to article

RNA Unknown sourcecode RNA123 Integrated platform for de novo and homology modeling of RNA 3D structures, where coordinate file input, sequence editing