Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computational prediction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources
PubMed2003

Protein family classification and functional annotation.

With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.

Amino Acid Motifs↗
PubMed2026

Senescent fibroblasts drive CD8+ T cell dysfunction in colorectal cancer via CD36-mediated lipid transfer and peroxidation.

BACKGROUND: Functional exhaustion of tumor-infiltrating CD8+ T cells represents a hallmark of colorectal cancer (CRC) immunosuppression, though its mechanistic drivers remain elusive. Given the established correlation between CRC progression and stromal senescence characterized by pathological lipid accumulation and impaired immunity, we investigated whether and how senescent fibroblasts actively regulate CD8+ T cell dysfunction. METHODS: Single-cell RNA sequencing (scRNA-seq) analysis was conducted to unveil the diverse fibroblast populations and the significant lipid metabolism changes between senescent fibroblasts and non-senescent fibroblasts in human CRC specimens and adjacent normal mucosa. Machine-learning identified senescent fibroblasts with a distinct gene signature. Cell-cell communication analysis was used to evaluate the interactions between senescent fibroblasts and CD8+ T cells in colorectal cancer. Co-culture experiments were conducted among senescent fibroblasts, CD8+ T cells and patient-derived organoids of CRC (CRC-PDOs), with the results evaluated with high-content imaging and propidium iodide/Hoechst 33,342 staining. Flow cytometry, ELISA and lipid pulse-chase with BODIPY FL C16 were performed to detect the alterations of CD8+ T cell cytotoxic function and metabolic status. AOM/DSS-induced CRC mouse model was used to conduct in vivo validation to evaluate whether senolytics could suppress CRC progression. Patients from the Cancer Genome Atlas colorectal cancer cohort were stratified into CD36-high and CD36-low groups by median expression, and drug sensitivity for GDSC2 compounds was predicted computationally using the oncoPredict R package. RESULTS: ScRNA-seq demonstrated the specific cell population presence and divergence of senescent fibroblasts between neoplastic and histologically normal adjacent cell clusters in CRC. Random Forest was employed for cell senescence classification. Feature importance analysis identified five genes as key contributors to the model’s decision process. Cell-cell communication analysis revealed enhanced interactions between senescent fibroblasts and CD8+ T cells in CRC. Co-culture of senescent fibroblasts significantly impaired the cytotoxic functions of CD8+ T cells on CRC-PDOs, which was reflected by the declined proportions of granzyme B (GZMB) + and interferon gamma (IFNγ) + CD8+ T cells and enhanced viability of CRC-PDOs. Mechanistically, the co-culture with senescent fibroblasts promoted the lipid shuttling into CD8+ T cells to induce lipid peroxidation and downstream impairment of cytotoxicity. Furthermore, the inhibition of CD36, the specific scavenger receptor for lipid uptake of CD8+ T cells, effectively suppressed lipid transfer and peroxidation thereby preserving the effector functions of CD8+ T cells and ultimately promoting tumor apoptosis. Complementarily, in vivo senolytic treatment significantly suppressed CRC progression in AOM-DSS CRC mouse models. Top 12 therapeutic agents were identified significantly enhanced predicted efficacy in CD36-high tumors. CONCLUSIONS: Our study identified a substantial population of senescent fibroblasts in human CRC through single cell transcriptomics, machine-learning and clinical biopsies. These senescent fibroblasts impair CD8+ T cell-mediated killing of CRC-PDOs via CD36-dependent lipid transfer, suggesting senolytic targeting of stromal cells as a promising immunotherapeutic strategy for CRC.

Colorectal Neoplasms↗
PubMed2001

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.

Peptide recognition modules mediate many protein-protein interactions critical for the assembly of macromolecular complexes. Complete genome sequences have revealed thousands of these domains, requiring improved methods for identifying their physiologically relevant binding partners. We have developed a strategy combining computational prediction of interactions from phage-display ligand consensus sequences with large-scale two-hybrid physical interaction tests. Application to yeast SH3 domains generated a phage-display network containing 394 interactions among 206 proteins and a two-hybrid network containing 233 interactions among 145 proteins. Graph theoretic analysis identified 59 highly likely interactions common to both networks. Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation.

Algorithms↗
PubMed2005

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

BACKGROUND: MicroRNAs (miRNAs) are a group of short (approximately 22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology. RESULTS: A set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM) is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information. CONCLUSION: The local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.

Animals↗
PubMed2005

Structural and functional study of the phenicol-specific efflux pump FloR belonging to the major facilitator superfamily.

The florfenicol-chloramphenicol resistance gene floR from Salmonella enterica was previously identified and postulated to belong to the major facilitator (MF) superfamily of drug exporters. Here, we confirmed a computer-predicted transmembrane topological model of FloR, using the phoA gene fusion method, and classified this protein in the DHA12 family (containing 12 transmembrane domains) of MF efflux transporters. We also showed that FloR is a transporter specific for structurally associated phenicol drugs (chloramphenicol, florfenicol, thiamphenicol) which utilizes the proton motive force to energize an active efflux mechanism. By site-directed mutagenesis of specific charged residues belonging to putative transmembrane segments (TMS), two residues essential for active efflux function, D23 in TMS1 and R109 in TMS4, were identified. Of these, the acidic residue D23 seems to participate directly in the affinity pocket involved in phenicol derivative recognition. A third residue, E283 in TMS9, seems to be necessary for correct membrane folding of the transporter.

Amino Acid Sequence↗
PubMed2004

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.

RegulonDB is the primary database of the major international maintained curation of original literature with experimental knowledge about the elements and interactions of the network of transcriptional regulation in Escherichia coli K-12. This includes mechanistic information about operon organization and their decomposition into transcription units (TUs), promoters and their sigma type, binding sites of specific transcriptional regulators (TRs), their organization into 'regulatory phrases', active and inactive conformations of TRs, as well as terminators and ribosome binding sites. The database is complemented with clearly marked computational predictions of TUs, promoters and binding sites of TRs. The current version has been expanded to include information beyond specific mechanisms aimed at gathering different growth conditions and the associated induced and/or repressed genes. RegulonDB is now linked with Swiss-Prot, with microarray databases, and with a suite of programs to analyze and visualize microarray experiments. We provide a summary of the biological knowledge contained in RegulonDB and describe the major changes in the design of the database. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/regulondb/.

Databases, Factual↗
PubMed2003

Virtual screening of virtual libraries.

Virtual screening of virtual libraries (VSVL) is a rapidly changing area of research. Great efforts are being made to produce better algorithms, selection methods and infrastructure. Yet, the number of successful examples in the literature is not impressive, although the quality of work certainly is high. Why is this? One reason is that these methods tend to be applied at the lead generation stage and therefore there is a large lead-time before successful examples appear in the literature. However, any computational chemist would confirm that these methods are successful and there exists a glut of start-up companies specialising in virtual screening. Moreover, the scientific community would not be focussing so much attention on this area if it were not yielding results. Even so, the paucity of literature data is certainly a hindrance to the development of better methods. The VSVL process is unique within the discovery process, in that it is the only method that can screen the > 10(30) genuinely novel molecules out there. Already, some VSVL methods are evaluating 10(13) compounds, a capacity that high throughput screening can only dream of. There is a huge potential advantage for the company that develops efficient and effective methods, for lead generation, lead hopping and optimization of both potency and ADME properties. To do this, it requires more than the software, it requires confidence to exploit the methodology, to commit synthesis on the basis of it, and to build this approach into the medicinal chemistry strategy. It is a fact that these tools remain quite daunting for the majority of scientists working at the bench. The routine use of these methods is not simply a matter of education and training. Integration of these methods into accessible and robust end user software, without dilution of the science, must be a priority. We have reached a coincidence, where several technologies have the required level of maturity predictive computational chemistry methods, algorithms that manage the combinatorial explosion, high throughput crystallography and ADME measurements and the massive increase in computational horsepower from distributed computing. The author is confident that the synergy of these technologies will bring great benefit to the industry, with more efficient production of higher quality clinical candidates. The future is bright. The future is virtual!

Algorithms↗
PubMed2000

Selectivity differences for C18 and C8 reversed-phase columns as a function of temperature and gradient steepness. I. Optimizing selectivity and resolution.

Four experimental runs where temperature T and gradient time tG are varied allow the computer-prediction of reversed-phase liquid chromatographic (RPLC) separation for different combinations of temperature and gradient time. This in turn can provide significant changes in selectivity and a resulting optimization of separation. If this procedure is repeated for different columns, additional control over selectivity and resolution becomes possible. The simultaneous variation of T and tG for columns from different sources was studied for two samples, as a means of evaluating the general advantage of this approach for RPLC method development. Changes in relative retention with T were found to be approximately constant for different values of tG and for different RPLC columns; similarly, changes in relative retention with tG were roughly independent of changes in temperature or the column. The latter relationships can be useful in matching ("tracking") peaks between runs during method development based on the present approach, as well as for other applications discussed in here and in Part II.

Chromatography, Liquid↗
PubMed2006

Molecular targets for rapid identification of Brucella spp.

BACKGROUND: Brucella is an intracellular pathogen capable of infecting animals and humans. There are six recognized species of Brucella that differ in their host preference. The genomes of the three Brucella species have been recently sequenced. Comparison of the three revealed over 98% sequence similarity at the protein level and enabled computational identification of common and differentiating genes. We validated these computational predictions and examined the expression patterns of the putative unique and differentiating genes, using genomic and reverse transcription PCR. We then screened a set of differentiating genes against classical Brucella biovars and showed the applicability of these regions in the design of diagnostic tests. RESULTS: We have identified and tested set of molecular targets that are associated in unique patterns with each of the sequenced Brucella spp. A comprehensive comparison was made among the published genome sequences of B. abortus, B. melitensis and B. suis. The comparison confirmed published differences between the three Brucella genomes, and identified subsets of features that were predicted to be of interest in a functional comparison of B. melitensis and B. suis to B. abortus. Differentiating sequence regions from B. abortus, B. melitensis and B. suis were used to develop PCR primers to test for the existence and in vitro transcription of these genes in these species. Only B. suis is found to have a significant number of unique genes, but combinations of genes and regions that exist in only two out of three genomes and are therefore useful for diagnostics were identified and confirmed. CONCLUSION: Although not all of the differentiating genes identified were transcribed under steady state conditions, a group of genes sufficient to discriminate unambiguously between B. suis, B. melitensis, and B. abortus was identified. We present an overview of these genomic differences and the use of these features to discriminate among a number of Brucella biovars.

Bacterial Typing Techniques↗
PubMed2005

Most nuclear systemic autoantigens are extremely disordered proteins: implications for the etiology of systemic autoimmunity.

Patients with systemic autoimmune diseases usually produce high levels of antibodies to self-antigens (autoantigens). The repertoire of common autoantigens is remarkably limited, yet no readily understandable shared thread links these apparently diverse proteins. Using computer prediction algorithms, we have found that most nuclear systemic autoantigens are predicted to contain long regions of extreme structural disorder. Such disordered regions would generally make poor B cell epitopes and are predicted to be under-represented as potential T cell epitopes. Consideration of the potential role of protein disorder may give novel insights into the possible role of molecular mimicry in the pathogenesis of autoimmunity. The recognition of extreme autoantigen protein disorder has led us to an explicit model of epitope spreading that explains many of the paradoxical aspects of autoimmunity - in particular, the difficulty in identifying autoantigen-specific helper T cells that might collaborate with the B cells activated in systemic autoimmunity. The model also explains the experimentally observed breakdown of major histocompatibility complex (MHC) class specificity in peptides associated with the MHC II proteins of activated autoimmune B cells, and sheds light on the selection of particular T cell epitopes in autoimmunity. Finally, the model helps to rationalize the relative rarity of clinically significant autoimmunity despite the prevalence of low specificity/low avidity autoantibodies in normal individuals.

Algorithms↗
PubMed1994

Improved field edge definition in electron arc therapy with dynamic collimation techniques.

PURPOSE: The diffuse shape of the electron beam used for arc therapy requires collimation on the patient's surface to sharply define treatment field edges. The electron beam arcs 10-15 degrees past field edges defined by a custom fitted and manufactured cast which acts as a tertiary collimator. This allows the entire beam profile to be integrated at the field edge. The tertiary collimator is heavy and bulky, requiring two therapists to lift and position the cast. An alternative technique for field edge definition would require the electron arc collimators to dynamically close to zero, while maintaining the projection of the leading edge of the field coincident with the geometric edge of the treatment field. This would allow integration of the entire electron arc profile and maintain a sharply defined treatment edge at the medial and lateral margins of the arc. The present customized cast could be replaced by generic lead strips at only the superior and inferior treatment field borders. This study investigates the dosimetry of dynamically collimated electron arc treatment volumes at field margins and its potential for eliminating the need for tertiary collimation at the arc field margins. METHODS AND MATERIALS: Electron arc isodose distributions were calculated using a pencil beam algorithm for treatment volumes defined by tertiary collimation at the surface of a cylindrical phantom and compared to distributions generated by simulating dynamic collimation to define the same field edges. Phantom measurements were performed using film densitometry to verify computer predictions. RESULTS: Penumbra width is one measure of the sharpness of dose fall off at a treatment field edge. We define it as the distance between the 90% and 20% isodose lines at the field edge measured orthogonal to the incident electron beam. Calculations and phantom film densitometry measurements were performed for electron energies from 6-20 MeV. Dynamic and tertiary collimation both reduce penumbra width by approximately 50% compared to no collimation. There is a small advantage in minimizing penumbra width at low electron energy with tertiary collimation. This shifts to a small advantage with dynamic collimation at high electron energy. CONCLUSION: Dynamic collimation produces a field edge isodose distribution equivalent to tertiary collimation for clinical purposes. These results suggest that tertiary collimation at medial and lateral electron are treatment field margins can be eliminated with dynamic collimation. This should result in greater clinical acceptance of breast electron arc therapy as the capacity for dynamic collimation is added to the next generation of linear accelerators.

Breast Neoplasms↗
PubMed2006

The TIGR Plant Transcript Assemblies database.

The TIGR Plant Transcript Assemblies (TA) database (http://plantta.tigr.org) uses expressed sequences collected from the NCBI GenBank Nucleotide database for the construction of transcript assemblies. The sequences collected include expressed sequence tags (ESTs) and full-length and partial cDNAs, but exclude computationally predicted gene sequences. The TA database includes all plant species for which more than 1000 EST or cDNA sequences are publicly available. The EST and cDNA sequences are first clustered based on an all-versus-all pairwise sequence comparison, followed by the generation of consensus sequences (TAs) from individual clusters. The clustering and assembly procedures use the TGICL tool, Megablast and the CAP3 assembler. The UniProt Reference Clusters (UniRef100) protein database is used as the reference database for the functional annotation of the assemblies. The transcription orientation of each TA is determined based on the orientation of the alignment with the best protein hit. The TA sequences and annotation are available via web interfaces and FTP downloads. Assemblies can be retrieved by a text-based keyword search or a sequence-based BLAST search. The current version of the TA database is Release 2 (July 17, 2006) and includes a total of 215 plant species.

DNA, Complementary↗
PubMed1997

Mutation of recombinant complement component C9 reveals the significance of the N-terminal region for polymerization.

Complement component C9 binds to C5b-8 sites on target cells and polymerizes to form the membrane attack complex (MAC). The aim of the work reported here was to discover which region within C9 was responsible for protecting the globular protein against self-polymerization. Computer prediction modelling highlighted the domain at the N-terminus of C9, which was then investigated by site-directed mutagenesis. The mutated proteins were expressed using insect cells infected with baculovirus. Removal of 16, 20 or 23 amino acids at the N-terminus of C9 resulted in inactivation due to self-polymerization. In contrast, removal of 4, 8 or 12 amino acids resulted in a C9 that did not polymerize spontaneously, had two to threefold enhanced lytic activity on erythrocytes, and had increased binding to C5b-8 sites on rat neutrophils. These results suggest that the domain within the first 16 amino acids at the N-terminus of C9 is crucial in preventing the self-polymerization of the globular protein. We have also found that C9 contains a motif (27WSEWS31) common to a family of cytokine receptors that is similar to a tryptophan-rich motif (WEWWR) of the membrane pore formers, thiol-activated cytolysins. Mutation of this motif in C9 resulted in polymerized protein, consistent with this site keeping the N-terminus in a protected conformation and preventing premature self-polymerization.

Amino Acid Sequence↗
PubMedDate not supplied

Study of local anesthetic activity of some derivatives of 3-amino-benzo-[d]-isothiazole.

On the basis of computer prediction of biological activity by PASS and toxicity by DEREK, the most prospective 18 alkylaminoacyl derivatives of 3-amino-benzo-[d]-isothiazole were selected. Their local anesthetic action was assessed using an in vitro preparation of the isolated peroneal nerve of the frog. The local anesthetics action of the compounds was assessed according to the time required for each compound to reduce the amplitude of the evoked compound action potential (CAP). Lidocaine was used as the control compound. The results show that the tested compounds can be divided into three groups: (a) compounds with action similar to lidocaine, (b) compounds with action lower than lidocaine and (c) compounds which block completely the evoked CAP, but after the compound was removed and replaced with normal saline showed no recovery of the potential at all. QSAR studies showed that polarizability, polarity and presence of five-membered rings in molecules have a positive influence on local anesthetic activity, while contributions of aromatic CH and singly bonded nitrogen are negative. Since estimations from PASS probabilities to find local anesthetic activity in the most active compounds were less than 50%, these compounds may be considered as new chemical entities (NCEs).

Action Potentials↗
PubMed2005

A peptide of human muscarinic acetylcholine receptor 3 is antigenic in primary Sjogren's syndrome.

To evaluate the antigenicity of a peptide representing a part of the second extracellular loop of the human muscarinic acetylcholine receptor 3 (m3AChR) with autoimmune sera from primary Sjogren's syndrome (pSS), enzyme-linked immunosorbent assays (ELISAs) were developed. On the basis of the computer-predicted data, a 16-mer synthetic peptide KRTVPPGECFIQFLSE (KRSE213-228) was produced by solid-phase peptide synthesis. cDNA coding for the KRSE peptide was chemically synthetized and utilized to express the recombinant glutathione S-transferase (GST)-KRSE fusion protein. The immunoreactivities of the two antigens were tested in ELISAs with the sera of 40 pSS patients and 40 healthy controls. The specificity of the reaction was confirmed by inhibition assays and immunoblottings. The pSS sera resulted in significantly higher mean optical densities than those of the healthy controls (KRSE: 0.4149 vs 0.1494, p<0.0001; GST-KRSE 0.4765 vs 0.1764, p<0.0001). The immunological recognition with the recombinant fusion antigen was significantly better than that for the free peptide (p=0.0068). The sensitivities of the assays were 77.5% (KRSE) and 97% (GST-KRSE). The results of the concentration-dependent inhibition assays by the two systems of peptide presentation indicated that the KRSE sequence is specific for pSS sera. This is the first demonstration of the antigenicity of a novel peptide fragment of the human m3AChR in pSS. The analysed peptide could be of diagnostic relevance.

Adult↗
PubMed1997

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water.

The folding of Ser-Tyr-Pro-Phe-Asp-Val (SYPFDV), and sequence variants of this peptide (SYPYD and SYPFD) are studied computationally in an explicit water environment. An atomically detailed model of the peptide is embedded in a sphere of TIP3P water molecules and its optimal structure is computed by simulated annealing. At distances from the peptide that are beyond a few solvation shells, a continuum solvent model is employed. The simulations are performed using a mean field approach that enhances the efficiency of sampling peptide conformations. The computations predict a small number of conformations as plausible folded structures. All have a type VI turn conformation for the peptide backbone, similar to that found using NMR. However, some of the structures differ from the experimentally proposed ones in the packing of the proline ring with the aromatic residues. The second most populated structure has, in addition to a correctly folded backbone, the same hydrophobic packing as the conformation measured by NMR. Our simulations suggest a kinetic mechanism that consists of three separate stages. The time-scales associated with these stages are distinct and depend differently on temperature. Electrostatic interactions play an initial role in guiding the peptide chain to a roughly correct structure as measured by the end-to-end distance. At the same time or later the backbone torsions rearrange due to local tendency of the proline ring to form a turn: this step depends on solvation forces and is helped by loose hydrophobic interactions. In the final step, hydrophobic residues pack against each other. We also show the existence of an off the pathway intermediate, suggesting that even in the folding of a small peptide "misfolded" structures can form. The simulations clearly show that parallel folding paths are involved. Our findings suggest that the process of peptide folding shares many of the features expected for the significantly larger protein molecules.

Computer Simulation↗
PubMed1996

Functional analysis of YCL09C: evidence for a role as the regulatory subunit of acetolactate synthase.

We have analysed the function of the open reading frame (ORF) YCL09C. The deletion of this ORF from chromosome III does not affect the physiology of the corresponding yeast strain enough to give a distinct phenotype. Nevertheless a computational analysis reveals high homology between this ORF and the enterobacterial genes encoding the regulatory subunit of acetolactate synthase. We have therefore tested the possibility that yc109cp is the regulatory subunit of yeast acetolactate synthase by in vitro enzymatic analysis. The acetolactate synthase was previously shown to be retroinhibited by its final product valine. In Escherichia coli this retro-control is assured by the regulatory subunit. Using a yeast strain carrying a complete deletion of YCL09C, we have observed the loss of such retro-inhibition. These results together with the computational predictions show that YCL09C encodes the regulatory subunit of yeast acetolactate synthase.

Acetoin↗
PubMed1996

Computational design of a substrate specificity mutant of a protein.

The wild-type trp repressor of E. coli bound 5-methoxytryptophan, a Trp analogue, less tightly than Trp. A mutant repressor (Val58-->Ala) that should bind 5-methoxytryptophan preferentially to Trp was computationally designed by free-energy calculations accompanied by free-energy decomposition. The designed mutant was demonstrated by experiments to bind 5-methoxytryptophan more tightly than Trp, consistent with the computational prediction. This success indicates the usefulness of free energy decomposition in protein design.

Bacterial Proteins↗